Commit 9b16e7c8 authored by Fabrice Allain's avatar Fabrice Allain Committed by Fabrice ALLAIN
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docs: Added link to example archive in docs

parent 40cbba1d
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
.. note::
Even if data for this example is already in the ``docs/examples`` folder. You
have to change at least ``cns_executable`` and ``host_executable`` with the
path of your CNS_ executable (not supplied in this package). Otherwise,
you cannot run this example.
.. 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
......@@ -26,14 +36,14 @@ The output should look like this
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 Checking if file 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 Reading secondary structure file 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 Reading distance file 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 Reader focused on file(s) ['examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out'] ['gremlin']
INFO Reading examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
INFO Filtering gremlin contact map
INFO ...Position filter
INFO Removed 21 contacts.
......@@ -47,29 +57,59 @@ The output should look like this
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
writing to the file: 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
MESSAGE [SequenceList]: reading sequence examples/bpt1/out/etc/BPT1_BOVIN.seq
reading 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 Dihedral restraints for secondary structures (examples/bpt1/out/tbl/BPT1_BOVIN_dihed.tbl)
INFO Secondary structure restraints (examples/bpt1/out/tbl/BPT1_BOVIN_ssdist.tbl)
INFO Helix bond restraints (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 Write 53 xml distance restraints in 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)
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
---
Once the setup step is done. We can run the generated ARIA_ project using the
command lines below
.. code-block:: console
aria2 -s examples/bpt1/out/ariaproject.xml
aria2 examples/bpt1/out/ariaproject.xml
.. warning::
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.
.. code-block:: console
aria2 --no-test examples/bpt1/out/ariaproject.xml
Analysis
--------
Here is a brief list of files you should look at when all the iteration are finished:
* 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)
A more detailed explanation of an ARIA output is on the main ARIA_ website.
.. _CNS: http://cns-online.org/v1.3/
.. _ARIA: http://aria.pasteur.fr
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