diff --git a/aria/conbox/conf/config.ini b/aria/conbox/conf/config.ini
index 05251f68fdd98df5c4de827440049b94aba8e911..74f24c0bb5c9016f23f132a84b26842835a52daf 100644
--- a/aria/conbox/conf/config.ini
+++ b/aria/conbox/conf/config.ini
@@ -36,7 +36,7 @@ default_cutoff:                             8.0
 ;ca_ca:
 ;cb_cb:
 ;sc_sc:
-
+bool
 [setup]
 ; ------------------------------ TBL parameters ------------------------------ #
 ; longrange_hb                  : True, False [False]
@@ -150,7 +150,7 @@ nd_alpha:                                   1.0
 runid:                                      1
 cpus:                                       100
 host_command:                               "sbatch -t 02:00:00"
-host_executable:                            bin/cns1.21_aria_logn_linux_x86_64_intel.exe
+host_executable:
 temp_root:                                  examples/tmp
 parameter_definition:                       automatic
 ss_dist_format:                             tbl
@@ -166,7 +166,7 @@ dist_calibrate:                             no
 dist_run_network_anchoring:                 no
 dist_filter_contributions:                  yes
 dist_avg_exponent:                          6
-cns_executable:                             bin/cns1.21.exe
+cns_executable:
 cns_keep_output:                            no
 unambiguous_restraints_k_cool1_initial:     10.0
 unambiguous_restraints_k_cool1_final:       50.0
diff --git a/aria/conbox/protmap.py b/aria/conbox/protmap.py
index d78299837971022b01ed98e0eaf38eef649ecc9d..37b7b7212162f1f7ad7e3098f10c339bfd411264 100644
--- a/aria/conbox/protmap.py
+++ b/aria/conbox/protmap.py
@@ -1017,7 +1017,6 @@ class ResAtmMap(ProteinMap):
         Returns
         -------
 
-        
         """
         if self._sequence:
             # If non empty string
@@ -1128,14 +1127,14 @@ class ResAtmMap(ProteinMap):
     def contact_map(self, contactdef, scsc_min=None, def_cut=5.0):
         """
         Contact map generator from all atoms distance map. There's a contact
-        with 2 residues iff dist between 2 atoms are below the given treshold
+        with 2 residues iff distance between 2 atoms are below the given treshold
 
         Parameters
         ----------
-        def_cut :
-            (Default value = 5.0)
+        def_cut : float
+            Default cutoff (Default value = 5.0)
         contactdef :
-            for all atom pair 
+            Contact definition for all atom pair
         scsc_min :
             (Default value = None)
 
diff --git a/docs/configuration.rst b/docs/configuration.rst
index 7862df5985d6254c85b4bb5a20245dbda8e72566..7f57e85af769a40eede92a52c4ca1959ee0c3dbe 100644
--- a/docs/configuration.rst
+++ b/docs/configuration.rst
@@ -18,11 +18,16 @@ configuration file should follow the `INI <https://en.wikipedia.org/wiki/INI_fil
 main
 ----
 
+.. note::
+
+  Leave these fields empty in order to use default files.
+
+
 .. rst-class:: table-hover
 
 +--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Name                     | Type | Default                                                                                  | Description                                                                                                                                                     |
-+--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
++==========================+======+==========================================================================================+=================================================================================================================================================================+
 | ss_dist_file             | path | :download:`ss_dist.txt <../aria/conbox/data/ss_dist.txt>`                                | Distances between stable secondary structures. Those distances are  used to make supplementary distance restraints related to secondary structure predictions.  |
 +--------------------------+------+------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | scsc_min_file            | path | :download:`scsc_min.p <../aria/conbox/data/scsc_min.p>`                                  |                                                                                                                                                                 |
@@ -54,23 +59,358 @@ main
 contactdef
 ----------
 
+Contact definition section used to define maplot from pdb file. More specific
+contact definitions can be added by following ``atomname_atomname`` syntax
+(e.g. ca_ca, cb_cb, ...) or ``sc_sc`` if we want to use a single treshold for
+side chain contacts defined in ``scsc_min_file``.
+
+.. rst-class:: table-hover
+
++----------------------------------+-------+---------+-------------------------------------------------------------------------------------------------------+
+| Name                             | Type  | Default | Description                                                                                           |
++==================================+=======+=========+=======================================================================================================+
+| default_cutoff                   | float | 8.0     | Default cutoff used for all type of contact. Decrease this threshold if using other cutoff (e.g. 5.0) |
++----------------------------------+-------+---------+-------------------------------------------------------------------------------------------------------+
+| atm1_atm2 (ca_ca, cb_cb, ...)    | float | None    | Specific treshold for a contact defined between atoms of two residues                                 |
++----------------------------------+-------+---------+-------------------------------------------------------------------------------------------------------+
+| sc_sc                            | float | None    | Default side chain atom treshold                                                                      |
++----------------------------------+-------+---------+-------------------------------------------------------------------------------------------------------+
+
 setup
 -----
 
+All the configuration parameters related to the ``setup`` command.
+
+.. rst-class:: table-hover
+
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Name                                         | Type                                                                   | Default                                      | Description                                                                                                                                                                                                                                                                                                                                                                             |
++==============================================+========================================================================+==============================================+=========================================================================================================================================================================================================================================================================================================================================================================================+
+| longrange_hb                                 | bool                                                                   | False                                        | use long range hbond restraints. If there is no hbond map given, use the naive method from METAPSICOV (Take the top nf_longrange_hb * seq length predicted contacts from the contactlist and set those who are in a beta sheet as hb                                                                                                                                                    |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| nf_longrange_hb                              | float                                                                  | 0.1                                          | Number hbond generated = nf * seq length                                                                                                                                                                                                                                                                                                                                                |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| longrange_hbtype                             | {main, all}                                                            | main                                         | Consider short range hbond only as main chain hydrogen bond or for all donor/acceptor                                                                                                                                                                                                                                                                                                   |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| hb_dminus                                    | float                                                                  | 0.0                                          | distance lower bound in tbl hbond restraints                                                                                                                                                                                                                                                                                                                                            |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| hb_dplus                                     | float                                                                  | 0.5                                          | distance upper bound in tbl hbond restraints                                                                                                                                                                                                                                                                                                                                            |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| native_reliable                              | bool                                                                   | False                                        | Define native contact map as reliable in aria iterative protocol. Those contacts will not be filtered                                                                                                                                                                                                                                                                                   |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| evfold_weight                                | bool                                                                   | False                                        | use EVFold weight -> 10/i (i:contact rank) for contact map derived distance restraints in aria protocol                                                                                                                                                                                                                                                                                 |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| neighborhood_contact                         | bool                                                                   | False                                        | Generate restraints for neighbors foreach contact in the contact map                                                                                                                                                                                                                                                                                                                    |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| atom_groups                                  | {all, heavy, min}                                                      | min                                          | use all, heavy atms or from a minimizedlist (CA, CB, SC) for contribution list for each distance restraint                                                                                                                                                                                                                                                                              |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| contributions_type                           | {same, allvsall, onevsall}                                             | same                                         | By default contributions list will be a simple list between atoms of the same type (CA-CA, CB-CB, ...). Otherwise, compute pairwise product between contribution lists of the 2 residues (onevsall and allvsall). In the case of ADR, onevsall will generate one ADR for all contribution pairs between an atom of the first residue against all the other atoms in the second residue. |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| distance_type                                | {fixed, pdbstat, distfile}                                             | fixed                                        | Define distance use for target distance. By default the target distance is fixed by parameters listed below. Otherwise a distance map derived from pdb distance distribution or given by the user can be used.                                                                                                                                                                          |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| groupby_method                               | {mean, min, deff}                                                      | min                                          | If a distance map is used for setting distance target, define if we use min, mean or deff distance on all the possible values.                                                                                                                                                                                                                                                          |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| deffpow                                      | int                                                                    | 6                                            |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| pdbdistance_level                            | {ss, res}                                                              | ss                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ambiguous_distance_restraint                 | bool                                                                   | False                                        | Generate Ambiguous Distance Restraints. Otherwise, each distance restraints will have only one contribution (unambiguous distance restraints)                                                                                                                                                                                                                                           |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| restraint_distance                           | float                                                                  | 2.5                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| lower_bound                                  | float                                                                  | 1.0                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| def_upper_bound                              | float                                                                  | 5.0                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ca_upper_bound                               | float                                                                  | 7.0                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| cb_upper_bound                               | float                                                                  | 7.0                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| n_factor                                     | float                                                                  | 1.0                                          | Factor used for selection of contacts according to their score (n * factor with n as sequence length)                                                                                                                                                                                                                                                                                   |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| contactfilter                                | all or combination of pos, cons, cys, ssclash separated by + character | all                                          | If empty, use only position filter (avoid short range restraints)                                                                                                                                                                                                                                                                                                                       |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| conservation_treshold                        | int                                                                    | 95                                           | Remove contact with highly conservated residues                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| position_treshold                            | int                                                                    | 5                                            | Remove short range contacts                                                                                                                                                                                                                                                                                                                                                             |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| seed                                         | int                                                                    | 89764443                                     | If no scoremap to select top n contacts, choose a subset with random.sample method. For reproductibility, the seed used for the sampling is provided here                                                                                                                                                                                                                               |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| net_deconv                                   | bool                                                                   | False                                        | use network deconvolution to filter contact map                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| nd_beta                                      | float                                                                  | 0.99                                         | eigenvalue scaling parameter for network deconvolution. Corresponding to propagation of indirect effects over longer indirect paths.                                                                                                                                                                                                                                                    |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| nd_alpha                                     | float                                                                  | 1.0                                          | Network density parameter corresponding to the use of the full mutual information and direct information matrices                                                                                                                                                                                                                                                                       |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| runid                                        | int                                                                    | 1                                            |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| cpus                                         | int                                                                    | 100                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| host_command                                 | str                                                                    | "sbatch -t 02:00:00"                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| host_executable                              | path                                                                   |                                              |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| temp_root                                    | path                                                                   | examples/tmp                                 |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| parameter_definition                         | {}                                                                     | automatic                                    |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ss_dist_format                               | {}                                                                     | tbl                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ss_dist_enabled                              | {yes, no}                                                              | yes                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ss_dist_add_to_network                       | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ss_dist_calibrate                            | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ss_dist_run_network_anchoring                | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ss_dist_filter_contributions                 | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| dist_format                                  | {}                                                                     | xml                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| dist_enabled                                 | {yes, no}                                                              | yes                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| dist_add_to_network                          | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| dist_calibrate                               | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| dist_run_network_anchoring                   | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| dist_filter_contributions                    | {yes, no}                                                              | yes                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| dist_avg_exponent                            | int                                                                    | 6                                            |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| cns_executable                               | path                                                                   |                                              |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| cns_keep_output                              | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| unambiguous_restraints_k_cool1_initial       | float                                                                  | 10.0                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| unambiguous_restraints_k_cool1_final         | float                                                                  | 50.0                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| unambiguous_restraints_k_cool2               | float                                                                  | 50.0                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| hbond_restraints_k_cool1_initial             | float                                                                  | 10.0                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| hbond_restraints_k_cool1_final               | float                                                                  | 50.0                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| hbond_restraints_k_cool2                     | float                                                                  | 50.0                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| dihedral_restraints_k_cool1                  | float                                                                  | 25.0                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| dihedral_restraints_k_cool2                  | float                                                                  | 200.0                                        |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| logharmonic_potential_enabled                | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| logharmonic_potential_use_auto_weight        | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| logharmonic_potential_weight_unambig         | float                                                                  | 25.0                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| logharmonic_potential_weight_ambig           | float                                                                  | 10.0                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| logharmonic_potential_weight_hbond           | float                                                                  | 25.0                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| rama_potential_enabled                       | {yes, no}                                                              | yes                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| hbdb_potential_enabled                       | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| scoring_method                               | {}                                                                     | standard                                     |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| md_parameters_random_seed                    | int                                                                    | 89764443                                     |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| md_parameters_steps_high                     | int                                                                    | 10000                                        |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| md_parameters_steps_cool1                    | int                                                                    | 5000                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| md_parameters_steps_cool2                    | int                                                                    | 4000                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| water_refinement_solvent                     | {}                                                                     | water                                        |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| water_refinement_n_structures                | int                                                                    | 10                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| water_refinement_enabled                     | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| water_refinement_write_solvent_molecules     | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| procheck_executable                          | path                                                                   |                                              |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| procheck_enabled                             | {yes, no}                                                              | yes                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| prosa_executable                             | path                                                                   |                                              |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| prosa_enabled                                | {yes, no}                                                              | yes                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| whatif_executable                            | path                                                                   |                                              |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| whatif_enabled                               | {yes, no}                                                              | yes                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| clashlist_executable                         | path                                                                   |                                              |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| clahlist_enabled                             | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| pickle_output                                | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| iterations                                   | int                                                                    | 8                                            |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| iteration_n_structures                       | int                                                                    | 100                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| iteration_sort_criterion                     | {}                                                                     | total_energy                                 |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| iteration_n_best_structures                  | int                                                                    | 15                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| iteration_n_kept_structures                  | int                                                                    | 0                                            |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| merging_method                               | {}                                                                     | standard                                     |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| calib_relaxation_matrix                      | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| calib_distance_cutoff                        | float                                                                  | 6.0                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| calib_estimator                              | {}                                                                     | ratio_of_averages                            |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| calib_error_estimator                        | {}                                                                     | distance                                     |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| viol_violation_tolerance                     | list of float                                                          | 1000.0,5.0,3.0,1.0,1.0,1.0,0.1,0.1,0.1       |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| viol_violation_threshold                     | float                                                                  | 0.5                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| viol_sigma_mode                              | {}                                                                     | fix                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| partassign_weight_threshold                  | list of float                                                          | 1.0,0.9999,0.999,0.99,0.98,0.96,0.93,0.9,0.8 |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| partassign_max_contributions                 | int                                                                    | 1000                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| partassign_exponent                          | int                                                                    | 6                                            |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| netanch_high_residue_threshold               | float                                                                  | 4.0                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| netanch_enabled                              | {yes, no}                                                              | no                                           |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| netanch_min_residue_threshold                | float                                                                  | 1.0                                          |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| netanch_min_atom_threshold                   | float                                                                  | 0.25                                         |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| clustering_enabled                           | {yes, no}                                                              | no                                           | Clustering step group generated structures into clusters. Cluster ensemble with the lowest energy will then be selected at the end of each iteration                                                                                                                                                                                                                                    |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| clustering_mask                              | {CA, CB}                                                               | CA                                           | Atom coordinate mask                                                                                                                                                                                                                                                                                                                                                                    |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| clustering_nclusters                         | int                                                                    | 2                                            | Number of clusters                                                                                                                                                                                                                                                                                                                                                                      |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| clustering_method                            | {kmeans, hclust, hdbscan}                                              | kmeans                                       |                                                                                                                                                                                                                                                                                                                                                                                         |
++----------------------------------------------+------------------------------------------------------------------------+----------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+
 maplot
 ------
 
+.. rst-class:: table-hover
+
++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+
+| Name                | Type          | Default                                         | Description                                             |
++=====================+===============+=================================================+=========================================================+
+| n_factors           | list of float | 0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.5,2.0 | Number of EC tested: n * n_factor (n: sequence length)  |
++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+
+| save_fig            | bool          | True                                            |                                                         |
++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+
+| heatmap_linewidths  | float         | 0.0                                             |                                                         |
++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+
+| size_fig            | int           | 10                                              |                                                         |
++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+
+| plot_ext            | {}            | pdf                                             |                                                         |
++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+
+| plot_dpi            | int           | 200                                             |                                                         |
++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+
+| alpha               | float         | 1.0                                             |                                                         |
++---------------------+---------------+-------------------------------------------------+---------------------------------------------------------+
+
 bbconv
 ------
 
+.. rst-class:: table-hover
+
++----------------+------+---------+-------------+
+| Name           | Type | Default | Description |
++================+======+=========+=============+
+| couplingmatrix |      |         |             |
++----------------+------+---------+-------------+
+| start          |      |         |             |
++----------------+------+---------+-------------+
+| end            |      |         |             |
++----------------+------+---------+-------------+
+| outputprefix   |      |         |             |
++----------------+------+---------+-------------+
+| PSIPREDfile    |      |         |             |
++----------------+------+---------+-------------+
+| diversityvalue |      |         |             |
++----------------+------+---------+-------------+
+| L              |      |         |             |
++----------------+------+---------+-------------+
+
 pdbqual
 -------
 
+.. rst-class:: table-hover
+
++------------------+------+---------+-------------+
+| Name             | Type | Default | Description |
++==================+======+=========+=============+
+| trash_directory  | path | /tmp    |             |
++------------------+------+---------+-------------+
+| prosa            | bool | False   |             |
++------------------+------+---------+-------------+
+| skip_prefix      | str  | fitted  |             |
++------------------+------+---------+-------------+
+| csh_executable   | path |         |             |
++------------------+------+---------+-------------+
+
 pdbdist
 -------
 
+.. rst-class:: table-hover
+
++---------------------+-------+---------------------+--------------------------------------+
+| Name                | Type  | Default             | Description                          |
++=====================+=======+=====================+======================================+
+| contact_cutoff      | float | 4.5                 | Cutoff used to search neighbor atoms |
++---------------------+-------+---------------------+--------------------------------------+
+| dssp_exec           | path  | /c6/shared/bin/dssp | Path of DSSP executable              |
++---------------------+-------+---------------------+--------------------------------------+
+| download_pdbs       | bool  | True                |                                      |
++---------------------+-------+---------------------+--------------------------------------+
+| obsolete_directory  | path  | /tmp/obsolete       |                                      |
++---------------------+-------+---------------------+--------------------------------------+
+| remove_pdbs         | bool  | False               |                                      |
++---------------------+-------+---------------------+--------------------------------------+
+| pair_list           | {}    | min                 |                                      |
++---------------------+-------+---------------------+--------------------------------------+
+
 pdbstat
 -------
 
+.. rst-class:: table-hover
+
++-----------------+----------------+------------+-----------------------------------------------------------------------------------------------------------------------------------------+
+| Name            | Type           | Default    | Description                                                                                                                             |
++=================+================+============+=========================================================================================================================================+
+| mode            | {simple}       | simple     | Extract minimal distance, mean of minimal mode, maximal distance from distance distribution to define bounds in serialized dictionaries |
++-----------------+----------------+------------+-----------------------------------------------------------------------------------------------------------------------------------------+
+| groups          | {ss,res,atm}   | ss+atm+res | Group levels in serialized dictionaries                                                                                                 |
++-----------------+----------------+------------+-----------------------------------------------------------------------------------------------------------------------------------------+
+| sample_minsize  | int            | 20         |                                                                                                                                         |
++-----------------+----------------+------------+-----------------------------------------------------------------------------------------------------------------------------------------+
+
 analysis
 --------
+
+.. rst-class:: table-hover
+
++---------------------+------------+---------------+-------------+
+| Name                | Type       | Default       | Description |
++=====================+============+===============+=============+
+| atmask              | {CA, CB}   | CA            |             |
++---------------------+------------+---------------+-------------+
+| violation_treshold  | float      | 0.5           |             |
++---------------------+------------+---------------+-------------+
+| nbest_structures    | int        | 15            |             |
++---------------------+------------+---------------+-------------+
+| sort_criterion      | {}         | total_energy  |             |
++---------------------+------------+---------------+-------------+
\ No newline at end of file
diff --git a/docs/examples/bpt1/bpt1.rst b/docs/examples/bpt1/bpt1.rst
index 21acce0b14bf070b3513ba645ba1269f841668b9..203341f562ced8d2d0b1fcfd1051042776ecad85 100644
--- a/docs/examples/bpt1/bpt1.rst
+++ b/docs/examples/bpt1/bpt1.rst
@@ -1,2 +1,75 @@
 BPT1_BOVIN structure prediction with EC map
 ===========================================
+
+Setup
+-----
+
+Here we show an example of setup with GREMLIN contacts with secondary structure
+prediction
+
+.. code-block:: console
+
+  ariaec -o examples/bpt1/out -c examples/bpt1/data/config.ini setup examples/bpt1/data/BPT1_BOVIN.fa examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out -t gremlin -s examples/bpt1/data/BPT1_BOVIN.indextableplus
+
+The output should look like this
+
+.. code-block:: console
+
+  ================================================================================
+
+                           ARIA Evolutive Contact toolbox
+
+  ================================================================================
+
+  INFO     Initialize settings
+  INFO     Updating settings according to config file
+  INFO     Making output directories
+  reading FASTA file examples/bpt1/data/BPT1_BOVIN.fa
+  INFO     Amino acid sequence:   FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
+  INFO     Checking if file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
+  INFO     Format type correct (indextableplus)
+  INFO     Reading secondary structure file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
+  INFO     Loading ss dist file
+  INFO     Reading distance file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/aria/conbox/data/ss_dist.txt
+  INFO     Align secondary structure sequence with protein sequence
+  INFO     Reader focused on file(s) ['/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out'] ['gremlin']
+  INFO     Reading /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
+  INFO     Filtering gremlin contact map
+  INFO     ...Position filter
+  INFO     Removed 21 contacts.
+  INFO     ...Conservation filter
+  INFO     Conservation filter only works with indextableplus files !
+  INFO     ...Secondary structure clash filter
+  INFO     Removed 1 contacts.
+  INFO     ...Disulfure bridge unicity filter
+  INFO     Removed 11 contacts.
+  INFO     Setting contact number with treshold 1.0
+  INFO     Update gremlin maplot
+  INFO     Update gremlin scoremap
+  INFO     Select top 53 contacts according to scoremap
+  writing to the file: /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN.seq
+  INFO     Load molecule file and convert it into xml format
+  MESSAGE [SequenceList]: reading sequence /baycells/home/fallain/Projects/ariaec/
+                          bin/python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN.
+                          seq
+                          reading /baycells/home/fallain/Projects/ariaec/bin/
+                          python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN.seq
+  INFO     Writing tbl files ...
+  INFO        Dihedral restraints for secondary structures (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/tbl/BPT1_BOVIN_dihed.tbl)
+  INFO        Secondary structure restraints (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/tbl/BPT1_BOVIN_ssdist.tbl)
+  INFO        Helix bond restraints (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/tbl/BPT1_BOVIN_hbond.tbl)
+  INFO     Writing gremlin ARIA XML distance restraints
+  INFO     Using contact scores as selection criteria
+  INFO     Selecting 53 contacts
+  INFO     0%|          | 0/53 [00:00<?, ?it/s]
+  INFO     100%|##########| 53/53 [00:00<00:00, 1485.97it/s]
+  INFO     Write 53 xml distance restraints in /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/xml/BPT1_BOVIN_gremlin.xml
+  INFO     Loading aria template file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/aria/conbox/templates/aria_project_v2.3.4.xml
+  INFO     Directory /tmp/BPT1_BOVIN/gremlin doesn't exist.
+  INFO     Create new directory /tmp/BPT1_BOVIN/gremlin
+  INFO     Writing ARIA project file (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/ariaproject.xml)
+  INFO     Generate contact file (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN_gremlin_filtered.contact.txt)
+
+Run
+---
+
diff --git a/docs/examples/bpt1/data/BPT1_BOVIN.fa b/docs/examples/bpt1/data/BPT1_BOVIN.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4259b24e02af6e580c01c52c6409f37c018eb974
--- /dev/null
+++ b/docs/examples/bpt1/data/BPT1_BOVIN.fa
@@ -0,0 +1,2 @@
+>sp|P00974|BPT1_BOVIN Pancreatic trypsin inhibitor OS=Bos taurus PE=1 SV=2
+FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
diff --git a/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus b/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus
new file mode 100644
index 0000000000000000000000000000000000000000..05a4ba779870ed0ec4c6698ae15986e8d2ad3d80
--- /dev/null
+++ b/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus
@@ -0,0 +1,101 @@
+up_index	up_residue	ss_pred	ss_conf	msa_index	msa_cons%	msa_cons	in_const	pdb_atom	pdb_chain	pdb_index	pdb_residue	pdb_x_pos	pdb_y_pos	pdb_z_pos
+1	M	C	9	-	-	-	-	-	-	-	-	-	-	-
+2	K	C	3	-	-	-	-	-	-	-	-	-	-	-
+3	M	H	2	-	-	-	-	-	-	-	-	-	-	-
+4	S	H	6	-	-	-	-	-	-	-	-	-	-	-
+5	R	H	7	-	-	-	-	-	-	-	-	-	-	-
+6	L	H	9	-	-	-	-	-	-	-	-	-	-	-
+7	C	H	9	-	-	-	-	-	-	-	-	-	-	-
+8	L	H	9	-	-	-	-	-	-	-	-	-	-	-
+9	S	H	9	-	-	-	-	-	-	-	-	-	-	-
+10	V	H	9	-	-	-	-	-	-	-	-	-	-	-
+11	A	H	9	-	-	-	-	-	-	-	-	-	-	-
+12	L	H	9	-	-	-	-	-	-	-	-	-	-	-
+13	L	H	9	-	-	-	-	-	-	-	-	-	-	-
+14	V	H	9	-	-	-	-	-	-	-	-	-	-	-
+15	L	H	9	-	-	-	-	-	-	-	-	-	-	-
+16	L	H	8	-	-	-	-	-	-	-	-	-	-	-
+17	G	H	6	-	-	-	-	-	-	-	-	-	-	-
+18	T	H	5	-	-	-	-	-	-	-	-	-	-	-
+19	L	H	1	-	-	-	-	-	-	-	-	-	-	-
+20	A	C	2	-	-	-	-	-	-	-	-	-	-	-
+21	A	C	7	-	-	-	-	-	-	-	-	-	-	-
+22	S	C	9	-	-	-	-	-	-	-	-	-	-	-
+23	T	C	9	-	-	-	-	-	-	-	-	-	-	-
+24	P	C	8	-	-	-	-	-	-	-	-	-	-	-
+25	G	C	9	-	-	-	-	-	-	-	-	-	-	-
+26	C	C	8	-	-	-	-	-	-	-	-	-	-	-
+27	D	C	7	-	-	-	-	-	-	-	-	-	-	-
+28	T	C	7	-	-	-	-	-	-	-	-	-	-	-
+29	S	C	6	-	-	-	-	-	-	-	-	-	-	-
+30	N	C	6	-	-	-	-	-	-	-	-	-	-	-
+31	Q	C	4	-	-	-	-	-	-	-	-	-	-	-
+32	A	C	1	-	-	-	-	-	-	-	-	-	-	-
+33	K	C	1	-	-	-	-	-	-	-	-	-	-	-
+34	A	C	4	-	-	-	*	-	-	-	-	-	-	-
+35	Q	C	9	-	-	-	*	-	-	-	-	-	-	-
+36	R	C	9	-	-	-	*	2	A	1	R	32.184	14.697	-11.772
+37	P	C	9	-	-	-	*	28	A	2	P	34.897	13.603	-9.390
+38	D	C	9	-	-	-	*	42	A	3	D	35.837	10.014	-9.507
+39	F	C	7	35	12	*	*	54	A	4	F	34.975	9.704	-5.855
+40	C	C	7	36	86	*	*	74	A	5	C	31.286	10.029	-6.794
+41	L	C	6	37	13	*	*	84	A	6	L	31.467	6.583	-8.351
+42	E	C	8	38	34	*	*	103	A	7	E	32.663	4.924	-5.112
+43	P	C	9	39	52	*	*	127	A	8	P	30.224	2.852	-3.086
+44	P	C	8	40	19	*	*	141	A	9	P	29.160	4.238	0.321
+45	Y	C	7	44	29	*	*	155	A	10	Y	31.512	3.320	3.156
+46	T	C	5	45	15	*	*	176	A	11	T	30.045	2.720	6.641
+47	G	C	6	46	82	*	*	190	A	12	G	33.523	2.128	8.130
+48	P	C	8	52	30	*	*	197	A	13	P	34.519	0.168	11.227
+49	C	C	7	56	85	*	*	211	A	14	C	32.817	2.337	13.956
+50	K	C	5	57	23	*	*	221	A	15	K	29.455	1.371	15.454
+51	A	C	3	63	30	*	*	243	A	16	A	27.519	4.598	15.454
+52	R	C	1	82	13	*	*	253	A	17	R	24.373	4.865	13.248
+53	I	E	5	83	15	*	*	277	A	18	I	24.709	8.341	11.537
+54	I	E	6	91	19	*	*	296	A	19	I	22.472	8.852	8.467
+55	R	E	5	92	54	*	*	315	A	20	R	24.442	10.455	5.670
+56	Y	E	4	93	45	*	*	339	A	21	Y	23.980	10.950	1.898
+57	F	E	5	96	49	*	*	360	A	22	F	25.997	9.344	-0.804
+58	Y	E	5	97	61	*	*	380	A	23	Y	25.779	9.725	-4.634
+59	N	E	5	98	44	*	*	401	A	24	N	24.473	6.511	-6.126
+60	A	C	4	111	17	*	*	415	A	25	A	25.937	6.771	-9.710
+61	K	C	9	112	12	*	*	425	A	26	K	23.844	3.843	-10.944
+62	A	C	9	113	28	*	*	447	A	27	A	20.576	5.701	-10.043
+63	G	C	9	114	25	*	*	457	A	28	G	21.970	9.249	-10.618
+64	L	C	1	115	18	*	*	464	A	29	L	20.589	10.458	-7.271
+65	C	E	5	116	99	*	*	483	A	30	C	21.875	11.033	-3.734
+66	Q	E	4	117	24	*	*	493	A	31	Q	20.508	8.474	-1.259
+67	T	E	7	121	15	*	*	510	A	32	T	20.941	7.836	2.490
+68	F	E	8	122	85	*	*	524	A	33	F	23.207	5.275	4.060
+69	V	E	7	125	19	*	*	544	A	34	V	24.349	4.496	7.646
+70	Y	E	2	127	73	*	*	560	A	35	Y	27.814	5.860	8.458
+71	G	C	4	131	54	*	*	581	A	36	G	29.544	4.252	11.487
+72	G	C	6	149	86	*	*	588	A	37	G	31.172	7.377	12.736
+73	C	C	7	151	86	*	*	595	A	38	C	34.813	7.212	11.868
+74	R	C	9	155	37	*	*	605	A	39	R	37.025	7.056	8.805
+75	A	C	9	157	80	*	*	629	A	40	A	34.631	8.632	6.385
+76	K	C	9	161	80	*	*	639	A	41	K	35.456	8.549	2.638
+77	R	C	8	165	14	*	*	661	A	42	R	34.659	11.372	0.167
+78	N	C	9	173	95	*	*	685	A	43	N	31.235	10.157	-1.075
+79	N	C	9	174	49	*	*	699	A	44	N	29.680	10.998	2.281
+80	F	C	3	175	90	*	*	713	A	45	F	27.732	14.188	2.696
+81	K	C	0	176	18	*	*	733	A	46	K	25.670	15.810	5.399
+82	S	C	3	177	48	*	*	755	A	47	S	23.068	17.191	3.061
+83	A	H	9	178	20	*	*	766	A	48	A	21.452	16.202	-0.192
+84	E	H	9	179	35	*	*	776	A	49	E	22.235	19.620	-1.652
+85	D	H	9	180	37	*	*	791	A	50	D	25.961	19.288	-1.082
+86	C	H	9	185	98	*	*	803	A	51	C	25.822	15.753	-2.493
+87	M	H	9	186	27	*	*	813	A	52	M	23.975	16.860	-5.592
+88	R	H	9	187	13	*	*	838	A	53	R	26.111	19.970	-6.044
+89	T	H	7	188	24	*	*	862	A	54	T	29.317	17.889	-5.933
+90	C	C	0	189	97	*	*	876	A	55	C	28.337	14.779	-7.839
+91	G	C	7	190	10	*	*	886	A	56	G	25.221	15.180	-9.791
+92	G	C	7	-	-	-	*	893	A	57	G	23.532	16.179	-13.038
+93	A	C	9	-	-	-	*	900	A	58	A	20.058	15.148	-14.143
+94	I	C	9	-	-	-	*	-	-	-	-	-	-	-
+95	G	C	9	-	-	-	*	-	-	-	-	-	-	-
+96	P	C	9	-	-	-	*	-	-	-	-	-	-	-
+97	W	C	9	-	-	-	-	-	-	-	-	-	-	-
+98	E	C	8	-	-	-	-	-	-	-	-	-	-	-
+99	N	C	9	-	-	-	-	-	-	-	-	-	-	-
+100	L	C	9	-	-	-	-	-	-	-	-	-	-	-
diff --git a/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out b/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out
new file mode 100644
index 0000000000000000000000000000000000000000..7f5016ed7a885bbbe5fa7f8815554eddab91b459
--- /dev/null
+++ b/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out
@@ -0,0 +1,81 @@
+i	j	i_id	j_id	r_sco	s_sco	prob
+11	35	11_C	35_C	1.8751	4.951	1.000
+17	41	17_R	41_N	1.2690	3.351	1.000
+21	28	21_N	28_Q	1.2309	3.250	1.000
+45	49	45_A	49_M	1.0435	2.755	1.000
+24	28	24_A	28_Q	0.8186	2.161	1.000
+14	31	14_R	31_V	0.8011	2.115	1.000
+6	19	6_P	19_F	0.7280	1.922	1.000
+18	45	18_Y	45_A	0.6058	1.600	0.998
+17	43	17_R	43_K	0.6022	1.590	0.998
+4	42	4_E	42_F	0.5441	1.437	0.995
+10	33	10_P	33_G	0.5022	1.326	0.991
+44	47	44_S	47_D	0.4921	1.299	0.990
+4	39	4_E	39_R	0.4679	1.235	0.985
+48	52	48_C	52_C	0.4673	1.234	0.985
+49	53	49_M	53_G	0.4665	1.232	0.984
+43	47	43_K	47_D	0.4617	1.219	0.983
+1	39	1_F	39_R	0.4528	1.196	0.981
+34	37	34_G	37_A	0.4515	1.192	0.980
+8	33	8_T	33_G	0.4497	1.188	0.980
+37	41	37_A	41_N	0.4362	1.152	0.975
+16	29	16_I	29_T	0.4345	1.147	0.974
+38	41	38_K	41_N	0.4193	1.107	0.968
+7	37	7_Y	37_A	0.4172	1.102	0.967
+19	28	19_F	28_Q	0.4127	1.090	0.964
+32	37	32_Y	37_A	0.4055	1.071	0.960
+46	50	46_E	50_R	0.3972	1.049	0.955
+10	36	10_P	36_R	0.3778	0.998	0.939
+47	51	47_D	51_T	0.3735	0.986	0.935
+9	37	9_G	37_A	0.3652	0.964	0.926
+9	41	9_G	41_N	0.3635	0.960	0.925
+25	53	25_G	53_G	0.3470	0.916	0.904
+30	38	30_F	38_K	0.3295	0.870	0.878
+1	51	1_F	51_T	0.3260	0.861	0.872
+16	31	16_I	31_V	0.3187	0.842	0.859
+1	42	1_F	42_F	0.3148	0.831	0.850
+15	31	15_I	31_V	0.3107	0.820	0.842
+3	22	3_L	22_A	0.3057	0.807	0.831
+3	45	3_L	45_A	0.2994	0.791	0.818
+11	33	11_C	33_G	0.2955	0.780	0.808
+32	40	32_Y	40_N	0.2914	0.769	0.797
+20	25	20_Y	25_G	0.2876	0.759	0.787
+13	34	13_A	34_G	0.2867	0.757	0.785
+8	12	8_T	12_K	0.2854	0.754	0.782
+14	33	14_R	33_G	0.2763	0.730	0.757
+32	41	32_Y	41_N	0.2761	0.729	0.756
+3	51	3_L	51_T	0.2701	0.713	0.738
+46	49	46_E	49_M	0.2698	0.712	0.737
+18	28	18_Y	28_Q	0.2615	0.691	0.713
+32	38	32_Y	38_K	0.2612	0.690	0.711
+5	23	5_P	23_K	0.2551	0.674	0.692
+18	29	18_Y	29_T	0.2549	0.673	0.691
+50	53	50_R	53_G	0.2540	0.671	0.688
+36	39	36_R	39_R	0.2507	0.662	0.677
+12	33	12_K	33_G	0.2468	0.652	0.664
+22	28	22_A	28_Q	0.2353	0.621	0.623
+25	28	25_G	28_Q	0.2341	0.618	0.618
+13	33	13_A	33_G	0.2299	0.607	0.603
+9	19	9_G	19_F	0.2286	0.604	0.599
+14	36	14_R	36_R	0.2260	0.597	0.590
+9	34	9_G	34_G	0.2240	0.592	0.583
+3	25	3_L	25_G	0.2200	0.581	0.567
+12	20	12_K	20_Y	0.2184	0.577	0.562
+23	29	23_K	29_T	0.2132	0.563	0.542
+20	27	20_Y	27_C	0.2089	0.552	0.526
+23	26	23_K	26_L	0.2037	0.538	0.507
+27	52	27_C	52_C	0.2036	0.538	0.507
+4	23	4_E	23_K	0.2036	0.538	0.507
+12	31	12_K	31_V	0.2023	0.534	0.501
+25	46	25_G	46_E	0.1989	0.525	0.488
+30	37	30_F	37_A	0.1986	0.524	0.487
+23	43	23_K	43_K	0.1985	0.524	0.487
+22	25	22_A	25_G	0.1900	0.502	0.456
+27	48	27_C	48_C	0.1895	0.500	0.454
+4	49	4_E	49_M	0.1872	0.494	0.445
+19	29	19_F	29_T	0.1832	0.484	0.432
+36	50	36_R	50_R	0.1802	0.476	0.421
+4	38	4_E	38_K	0.1800	0.475	0.420
+3	47	3_L	47_D	0.1798	0.475	0.420
+8	31	8_T	31_V	0.1765	0.466	0.408
+30	33	30_F	33_G	0.1755	0.463	0.404
diff --git a/docs/examples/bpt1/data/config.ini b/docs/examples/bpt1/data/config.ini
index 24ad5a6944b251d2ec59dc4315ee8ec7dd1e225c..d44c73e864e8bd02fd7001d889628e9bd9f5766b 100644
--- a/docs/examples/bpt1/data/config.ini
+++ b/docs/examples/bpt1/data/config.ini
@@ -10,7 +10,7 @@ n_factor:                                   1.0
 host_command:                               sbatch -t 06:00:00
 host_executable:                            /path/to/cns1.21.exe
 cns_executable:                             /path/to/cns1.21.exe
-temp_root:                                  /path/to/tempdir
+temp_root:                                  /tmp
 # Protocol parameters
 # -------------------
 rama_potential_enabled:                     yes
diff --git a/docs/tutorial/analysis.rst b/docs/tutorial/analysis.rst
index 88282d21fc2b40e731a05588ca110daed03ecc8a..63fb6b45e3be6e75b174ee383aa66685bae6a787 100644
--- a/docs/tutorial/analysis.rst
+++ b/docs/tutorial/analysis.rst
@@ -1,2 +1,5 @@
 Analysis
 ========
+
+Analyse des cartes de contacts via la commande maplot
+Analyse de structures au format PDB via la commande pdbqual (en ayant précisé les chemins des programmes dans le fichier de configuration)
diff --git a/docs/tutorial/run.rst b/docs/tutorial/run.rst
index 332cd5431a5c529606b8b9fed71dd902dd719b5b..5d3a1e5f23f6be0c03760d5b38560524b49a5e4e 100644
--- a/docs/tutorial/run.rst
+++ b/docs/tutorial/run.rst
@@ -1,2 +1,7 @@
 Run
 ===
+
+Cette étape se résume en deux partie,
+L'initialisation du projet ARIA généré durant le setup
+L'exécution du projet
+=> NB vérifier la commande utilisée pour exécuter le projet si elle correspond au gestionnaire de job utilisé par votre cluster
diff --git a/docs/tutorial/setup.rst b/docs/tutorial/setup.rst
index 1f6b43aa54305580689fa0edca64ae3b559808ce..5d0934b1e21803b131e789547a6ac957e4bdb10c 100644
--- a/docs/tutorial/setup.rst
+++ b/docs/tutorial/setup.rst
@@ -1,3 +1,7 @@
 Setup
 =====
 
+Modifier les paramètres indiquant le chemin de CNS et du ou des programmes d'analyse qu'on souhaite utiliser
+Lancer la commande setup en prenant en compte l'ensemble des fichiers qu'on souhaite convertir
+Lister les différents fichiers générés
+Verifier dans les log si les étapes se sont correctement déroulé
diff --git a/docs/usage.rst b/docs/usage.rst
index ea6aae38bd8d9124eaec25efb5d1248af6c80761..005043b4ea1d20c75b0b28409b4b4e46e7d8fb78 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -27,7 +27,7 @@ ARIAEC
 
 +-------------------------+-----------------------------------------------------+
 |  Name                   | Short description                                   |
-+-------------------------+-----------------------------------------------------+
++=========================+=====================================================+
 | `setup <Setup_>`_       | Setup ARIA project with EC data                     |
 +-------------------------+-----------------------------------------------------+
 | `bbconv <BBconv_>`_     | Translate BBcontacts as distance restraints         |
@@ -56,7 +56,7 @@ ARIAEC
 
 +--------------------------------------------------------+-----------------------------------------------------+
 |  Name                                                  | Description                                         |
-+--------------------------------------------------------+-----------------------------------------------------+
++========================================================+=====================================================+
 | ``-h``, ``--help``                                     | show help message and exit                          |
 +--------------------------------------------------------+-----------------------------------------------------+
 | ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None)                    |
@@ -86,7 +86,7 @@ Translate contact maps as distance restraints and setup ARIA infrastructure.
 
 +-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 |  Name                   | Short description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
++=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
 | ``seq``                 | Sequence file [``FASTA``]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
 +-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``infile``              | Contact or pdb file(s) used to build aria distance restraints                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
@@ -107,7 +107,7 @@ Translate contact maps as distance restraints and setup ARIA infrastructure.
 
 +--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
 |  Name                                                  | Description                                                                                                                                            |
-+--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
++========================================================+========================================================================================================================================================+
 | ``-d DISTFILE``, ``--distfile DISTFILE``               | Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints |
 +--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``-s SSPRED``, ``--ssfile SSPRED``                     | Secondary structure prediction file                                                                                                                    |