Commit 48771310 authored by Fabrice Allain's avatar Fabrice Allain
Browse files

docs: Added MALE_ECOLI example data

parent 9ec966ba
......@@ -2,6 +2,7 @@
## <small>0.0.18 (2018-04-23)</small>
* docs: Added bpt1 setup in examples ([a76abff](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a76abff))
* docs: updated changelog ([ceececc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ceececc))
* docs: updated changelog ([95d3f62](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/95d3f62))
* docs: Updated changelog (removed old tags) ([a59416d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a59416d))
* Added casp rr support when there is no header (pfrmatrr) ([d9d7349](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d9d7349))
......
......@@ -41,10 +41,6 @@ Then the easiest solution is to call the **pip** command below :
``pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec``
Even though it is not recommanded, another possibility is to download the ZIP_
or TAR_ version from Gitlab_, extract the files and run ``pip install .``
inside the new directory.
For more information about installation and usage, please refer to the
`ARIAEC documentation <http://bis-aria.pages.pasteur.fr/ariaec>`_.
......
BPT1_BOVIN structure prediction with EC map
===========================================
The files related to this example can be found in the ``docs`` folder or
:download:`here <docs/examples.tar.gz>`
Setup
-----
Here we show an example of setup with GREMLIN contacts with secondary structure
prediction
Here we show an example of *de novo* structure prediction from GREMLIN contacts
combined with secondary structure prediction. The files related to this example
can be found in the ``docs`` folder or :download:`here <docs/examples.tar.gz>`.
.. note::
......@@ -17,9 +12,19 @@ prediction
path of your CNS_ executable (not supplied in this package). Otherwise,
you cannot run this example.
Contact map analysis
--------------------
.. 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
> ariaec -o examples/bpt1/out maplot examples/bpt1/data/BPT1_BOVIN.fa examples/bpt1/data/BPT1_BOVIN.indextableplus examples/bpt1/.native.aligned.pdb $< -t pdb contactlist maplot --onlyreport $(DATADIR)/$${prot}/$${prot}.fa $${psipred_file} $(DATADIR)/$${prot}/$${prot}.native.aligned.pdb $< -t pdb contactlist
Setup
-----
.. 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
......@@ -77,39 +82,152 @@ The output should look like this
INFO Writing ARIA project file (examples/bpt1/out/ariaproject.xml)
INFO Generate contact file (examples/bpt1/out/etc/BPT1_BOVIN_gremlin_filtered.contact.txt)
Run
---
ARIA Setup
----------
.. code-block:: console
Once the setup step is done. We can run the generated ARIA_ project using the
command lines below
> aria2 -s examples/bpt1/out/ariaproject.xml
.. code-block:: console
aria2 -s examples/bpt1/out/ariaproject.xml
aria2 examples/bpt1/out/ariaproject.xml
ARIA Version 2.3.2. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.
.. warning::
If you use this software, please quote the following reference(s):
Depending on your environment, you probably have to give ``--no-test`` option
for the second command in order to disable the dry run of the commands
specified for the structure calculation.
Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
structure calculation. Bioinformatics 23:381-382
.. code-block:: console
aria2 --no-test examples/bpt1/out/ariaproject.xml
Loading project "ariaproject.xml"...
Setting-up examples/bpt1/out/ariaproject.xml (run: 1)
MESSAGE [Project]: Protocols copied.
MESSAGE [Project]: Directory tree created.
MESSAGE [Project]: Copying data files into local data-directory...
Analysis
Done.
For running ARIA: aria2 examples/bpt1/out/ariaproject.xml
ARIA Run
--------
Here is a brief list of files you should look at when all the iteration are finished:
.. code-block:: console
> aria2 examples/bpt1/out/ariaproject.xml
* ARIA ensemble for each iteration. Depending of the activation of the water refinment step, the last ensemble is located within ``runX/structures/itY`` or ``runX/structures/refine`` folder (X is the number related to the last iteration).
* ``report`` (and ``report.clustering`` if clustering is activated) related to ensemble of generated structure
* ``itY/analysis`` folder with all structure quality reports generated with Procheck, molprobity, whatif & prosa (iff the executable path are correct in the initial configuration file)
.. code-block:: console
ARIA Version 2.3.2. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.
If you use this software, please quote the following reference(s):
Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
structure calculation. Bioinformatics 23:381-382
Loading project "ariaproject.xml"...
MESSAGE [Project]: Temporary directory has been set to /tmp/BPT1_BOVIN/gremlin/
aria_temp.tmpw0BTnZ1524489605
MESSAGE [Project]: Host list check has been disabled.
MESSAGE [Project]: -------------------- Reading data --------------------
MESSAGE [Project]: Cache is enabled.
MESSAGE [Project]: Cache file does not exist. Creating new file.
MESSAGE [Project]: Reading molecule definition examples/bpt1/out/run1/data/
sequence/BPT1_BOVIN.xml.
MESSAGE [Project]: Data files read.
MESSAGE [Project]: Data files cached.
MESSAGE [Project]: ------------------- Filtering input data -------------------
MESSAGE [NOESYSpectrumFilter.TP]: Spectrum filter report written to file "
examples/bpt1/out/run1/data/spectra/
peak_list.filtered"
MESSAGE [Project]: ---------------- Preparing structure engine ----------------
MESSAGE [CNS]: Sequence PDB-file written.
MESSAGE [CNS]: PSF-file has been created.
MESSAGE [CNS]: Template PDB-file has been created.
MESSAGE [Project]: Starting ARIA main protocol on Mon Apr 23 15:20:31 2018
MESSAGE [Project]: -------------------- Assigning spectra --------------------
MESSAGE [Protocol]: ---------------------- Iteration 0 -----------------------
MESSAGE [Protocol]: Calibrating spectrum "gremlin"...
MESSAGE [Job]: Submitted batch job 18432586 (run_cns_99)
MESSAGE [Job]: Submitted batch job 18432587 (run_cns_96)
...
MESSAGE [CNS]: Starting analyses...
MESSAGE [CNS]: Analyses done. Results are in examples/bpt1/out/run1/structures/
it8/analysis
MESSAGE [Project]: Temporary directory "/baycells/scratch/fallain/tmp/
BPT1_BOVIN/gremlin/aria_temp.tmpRNyO3Q1524493463" removed.
MESSAGE [Project]: ARIA run completed at Mon Apr 23 17:25:08 2018
Violation analysis
------------------
Violation analysis for the last iteration
A more detailed explanation of an ARIA output is on the main ARIA_ website.
.. code-block:: console
> ariaec -c examples/bpt1/data/config.ini -o examples/bpt1/out/run1/structures/it8 analysis -r examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb examples/bpt1/out/ariaproject.xml examples/bpt1/out/run1/structures/it8 gremlin
**Output**
.. code-block:: console
================================================================================
ARIA Evolutive Contact toolbox
================================================================================
INFO Initialize settings
INFO Updating settings according to config file
INFO Reading distance restraints file(s)
INFO Wrote 143 xml distance restraints in examples/bpt1/out/run1/structures/it0/unambig_restraints.xml
INFO Reading native structure
MESSAGE [StructureEnsemble]: Reading PDB files ...
MESSAGE [StructureEnsemble]: PDB files read.
INFO Reading structure ensemble(s)
INFO Clusters found in this iteration, compute analysis foreach generated cluster ensemble
INFO Violation analysis
INFO Writing violation analysis of clust 0 examples/bpt1/out/run1/structures/it0/violations.csv file
INFO Writing violation analysis of clust 1 examples/bpt1/out/run1/structures/it0/violations.csv file
MESSAGE [StructureEnsemble]: Reading PDB files ...
MESSAGE [StructureEnsemble]: PDB files read.
.. _CNS: http://cns-online.org/v1.3/
.. _ARIA: http://aria.pasteur.fr
.. raw:: html
<style>
.panel {
padding: 0 18px;
background-color: white;
max-height: 0;
overflow: hidden;
transition: max-height 0.2s ease-out;
}
</style>
<script>
var acc = document.getElementsByClassName("accordion");
var i;
for (i = 0; i < acc.length; i++) {
acc[i].addEventListener("click", function() {
this.classList.toggle("active");
var panel = this.nextElementSibling;
if (panel.style.maxHeight){
panel.style.maxHeight = null;
} else {
panel.style.maxHeight = panel.scrollHeight + "px";
}
});
}
</script>
\ No newline at end of file
This diff is collapsed.
......@@ -8,9 +8,9 @@ n_factor: 1.0
# ARIA project parameters
# -----------------------
host_command: sbatch -t 06:00:00
host_executable: /path/to/cns1.21.exe
cns_executable: /path/to/cns1.21.exe
temp_root: /tmp
host_executable: /PATH/TO/CNS
cns_executable: /PATH/TO/CNS
temp_root: /PATH/TO/TMP
# Protocol parameters
# -------------------
rama_potential_enabled: yes
......@@ -19,7 +19,7 @@ md_parameters_steps_high: 20000
md_parameters_steps_cool1: 100000
md_parameters_steps_cool2: 80000
md_parameters_random_seed: 89764443
procheck_executable: /path/to/procheck
whatif_executable: /path/to/whatif
procheck_executable: /PATH/TO/PROCHECK
whatif_executable: /PATH/TO/WHATIF
clustering_enabled: yes
clustering_nclusters: 2
>/baycells/home/fallain/Projects/ariaec/data/2017-04-ECNMR/MALE_ECOLI/MALE_ECOLI.native.aligned | chain A | 370 aa
KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDII
FWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKD
LLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKD
VGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKV
NYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLG
AVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEA
LKDAQTRITK
This source diff could not be displayed because it is too large. You can view the blob instead.
<!DOCTYPE project SYSTEM "project1.0.dtd">
<project name="MALE_ECOLI" version="1.0" author="" date="" description="" comment="" references="" working_directory="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI" temp_root="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI" run="1" file_root="MALE_ECOLI" cache="yes" cleanup="yes">
<data>
<ccpn_model filename=""/>
<molecule file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/sequence.xml" format="xml" ccpn_id="">
<linkage_definition name="automatic" filename=""/>
<parameter_definition name="automatic" filename=""/>
<topology_definition name="automatic" filename=""/>
</molecule>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/n20_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/n20_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="0.025" freq_window_hetero1="0.3" freq_window_proton2="0.04" freq_window_hetero2="0.5" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/c_redo_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/c_redo_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="0.025" freq_window_hetero1="0.3" freq_window_proton2="0.04" freq_window_hetero2="0.5" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/cc20_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/cc20_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/nn20_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/nn20_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/cn0_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/cn0_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/nc0_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/nc0_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<rdcs file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/gel_exp.tbl" format="tbl" ccpn_id="" enabled="yes" parameter_class="1"/>
<dihedrals file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/talos.tbl" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/>
<symmetry enabled="no" method="standard" n_monomers="1" symmetry_type="None" ncs_enabled="no" packing_enabled="no"/>
<initial_structure file="" format="iupac" ccpn_id="" enabled="no"/>
</data>
<structure_generation engine="cns">
<cns local_executable="/baycells/home/bardiaux/Progs/aria2.3.2_hbdb/cns1.21_aria_logn_hbdb_linux_x86_64_intel.exe" keep_output="no" keep_restraint_files="yes" create_psf_file="yes" generate_template="yes" nonbonded_parameters="PROLSQ">
<annealing_parameters>
<unambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" k_cool1_final="50.0" k_cool2="50.0"/>
<ambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" k_cool1_final="50.0" k_cool2="50.0"/>
<hbond_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" k_cool1_final="50.0" k_cool2="50.0"/>
<dihedral_restraints k_hot="5.0" k_cool1="25.0" k_cool2="200.0"/>
<karplus_restraints parameter_class="1" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
<karplus_restraints parameter_class="2" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
<karplus_restraints parameter_class="3" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
<karplus_restraints parameter_class="4" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
<karplus_restraints parameter_class="5" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0"/>
<rdc_restraints parameter_class="1" method="SANI" first_iteration="4" k_hot="0.0" k_cool1="0.02" k_cool2="0.5" r="0.157" d="17.536" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
<rdc_restraints parameter_class="2" method="SANI" first_iteration="0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
<rdc_restraints parameter_class="3" method="SANI" first_iteration="0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
<rdc_restraints parameter_class="4" method="SANI" first_iteration="0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
<rdc_restraints parameter_class="5" method="SANI" first_iteration="0" k_hot="0.0" k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" center_cool2_final="10.0"/>
<flat_bottom_harmonic_wall m_rswitch_hot="0.5" m_rswitch_cool1="0.5" m_rswitch_cool2="0.5" rswitch_hot="0.5" rswitch_cool1="0.5" rswitch_cool2="0.5" m_asymptote_hot="-1.0" m_asymptote_cool1="-1.0" m_asymptote_cool2="-0.1" asymptote_hot="1.0" asymptote_cool1="1.0" asymptote_cool2="0.1"/>
<symmetry_restraints k_packing_hot="15.0" k_packing_cool1="10.0" k_packing_cool2="5.0" last_iteration_packing="8" k_ncs="50.0"/>
<logharmonic_potential enabled="no" use_auto_weight="no" weight_unambig="25.0" weight_ambig="25.0" weight_hbond="25.0"/>
<rama_potential enabled="no" weight_rama="1.0"/>
</annealing_parameters>
<md_parameters dynamics="torsion" random_seed="89764443" tad_temp_high="10000.0" tad_timestep_factor="9.0" cartesian_temp_high="2000.0" cartesian_first_iteration="0" timestep="0.003" temp_cool1_final="1000.0" temp_cool2_final="50.0" steps_high="20000" steps_refine="4000" steps_cool1="30000" steps_cool2="30000"/>
</cns>
<job_manager default_command="csh -f">
<host enabled="yes" command="qsub -@ /Bis/home/bardiaux/sge_options.sge" executable="" n_cpu="60" use_absolute_path="yes"/>
</job_manager>
</structure_generation>
<protocol floating_assignment="yes">
<iteration number="0" n_structures="100" sort_criterion="total_energy" n_best_structures="15" n_kept_structures="0">
<assignment/>
<merging method="combination4_4"/>
<calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
<violation_analysis sigma_mode="fix" violation_tolerance="1000.0" violation_threshold="0.5"/>
<partial_assignment weight_threshold="1.0" max_contributions="20"/>
<network_anchoring high_residue_threshold="4.0" enabled="yes" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
</iteration>
<iteration number="1" n_structures="100" sort_criterion="total_energy" n_best_structures="15" n_kept_structures="0">
<assignment/>
<merging method="combination4_4"/>
<calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
<violation_analysis sigma_mode="fix" violation_tolerance="5.0" violation_threshold="0.5"/>
<partial_assignment weight_threshold="0.9999" max_contributions="20"/>
<network_anchoring high_residue_threshold="4.0" enabled="yes" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
</iteration>
<iteration number="2" n_structures="100" sort_criterion="total_energy" n_best_structures="15" n_kept_structures="0">
<assignment/>
<merging method="combination4_4"/>
<calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
<violation_analysis sigma_mode="fix" violation_tolerance="3.0" violation_threshold="0.5"/>
<partial_assignment weight_threshold="0.999" max_contributions="20"/>
<network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
</iteration>
<iteration number="3" n_structures="100" sort_criterion="total_energy" n_best_structures="15" n_kept_structures="0">
<assignment/>
<merging method="standard"/>
<calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
<violation_analysis sigma_mode="fix" violation_tolerance="1.0" violation_threshold="0.5"/>
<partial_assignment weight_threshold="0.99" max_contributions="20"/>
<network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
</iteration>
<iteration number="4" n_structures="100" sort_criterion="total_energy" n_best_structures="15" n_kept_structures="0">
<assignment/>
<merging method="standard"/>
<calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
<violation_analysis sigma_mode="fix" violation_tolerance="1.0" violation_threshold="0.5"/>
<partial_assignment weight_threshold="0.98" max_contributions="20"/>
<network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
</iteration>
<iteration number="5" n_structures="100" sort_criterion="total_energy" n_best_structures="15" n_kept_structures="0">
<assignment/>
<merging method="standard"/>
<calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
<violation_analysis sigma_mode="fix" violation_tolerance="1.0" violation_threshold="0.5"/>
<partial_assignment weight_threshold="0.96" max_contributions="20"/>
<network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
</iteration>
<iteration number="6" n_structures="100" sort_criterion="total_energy" n_best_structures="15" n_kept_structures="0">
<assignment/>
<merging method="standard"/>
<calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
<violation_analysis sigma_mode="fix" violation_tolerance="0.1" violation_threshold="0.5"/>
<partial_assignment weight_threshold="0.93" max_contributions="20"/>
<network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
</iteration>
<iteration number="7" n_structures="100" sort_criterion="total_energy" n_best_structures="15" n_kept_structures="0">
<assignment/>
<merging method="standard"/>
<calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
<violation_analysis sigma_mode="fix" violation_tolerance="0.1" violation_threshold="0.5"/>
<partial_assignment weight_threshold="0.9" max_contributions="20"/>
<network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
</iteration>
<iteration number="8" n_structures="100" sort_criterion="total_energy" n_best_structures="15" n_kept_structures="0">
<assignment/>
<merging method="standard"/>
<calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" error_estimator="distance"/>
<violation_analysis sigma_mode="fix" violation_tolerance="0.1" violation_threshold="0.5"/>
<partial_assignment weight_threshold="0.8" max_contributions="20"/>
<network_anchoring high_residue_threshold="4.0" enabled="no" min_residue_threshold="1.0" min_atom_threshold="0.25"/>
</iteration>
<water_refinement solvent="water" n_structures="15" enabled="yes" write_solvent_molecules="no"/>
</protocol>
<analysis>
<structures_analysis enabled="yes"/>
<procheck executable="procheck" enabled="yes"/>
<prosa executable="prosa" enabled="yes"/>
<whatif executable="whatif" enabled="yes"/>
<clashlist executable="" enabled="no"/>
</analysis>
<report>
<ccpn export_assignments="no" export_noe_restraint_list="no" export_structures="no"/>
<molmol enabled="yes"/>
<noe_restraint_list pickle_output="no" text_output="yes" xml_output="no"/>
<spectra write_assigned="no" write_assigned_force="no" iteration="last" write_unambiguous_only="yes"/>
</report>
</project>
\ No newline at end of file
......@@ -8,9 +8,9 @@ n_factor: 1.0
# ARIA project parameters
# -----------------------
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
host_executable: /baycells/home/fallain/Applications/CNS/cns1.21_aria_logn_hbdb_linux_x86_64_intel.exe
cns_executable: /baycells/home/fallain/Applications/CNS/cns1.21_aria_logn_hbdb_linux_x86_64_intel.exe
temp_root: /baycells/scratch/fallain/tmp
# Protocol parameters
# -------------------
rama_potential_enabled: yes
......
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