Determination of the protein state populations - Revision history

Dima: /* Execution */

2021-09-07T11:42:47Z

Execution

← Older revision		Revision as of 13:42, 7 September 2021
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	Check that '''init.cya''' and '''CALC.cya''' have '''rmsdrange''' variable (range to calculate RMSD of the protein bundle) set to correct value		Check that '''init.cya''' and '''CALC.cya''' have '''rmsdrange''' variable (range to calculate RMSD of the protein bundle) set to correct value

	Check that '''~~SPLIT~~.cya''' has '''nres''' variable (number of residues) set to correct value		Check that '''SPLITpop.cya''' has '''nres''' variable (number of residues) set to correct value. Keep in mind that in this case SPLITpop only takes one sample from the population A and population B. This means that SPLITpop will output a PDB with 40 conformers in 40 separate PDB models given both states A and B are populated or 20 conformers in 20 separate PDB models otherwise.

	Then, test the '''data/''' folder by running a test calculation:		Then, test the '''data/''' folder by running a test calculation:

Dima: /* Execution */

2021-09-07T11:30:58Z

Execution

← Older revision		Revision as of 13:30, 7 September 2021
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	If you do not have an access to parallel computation change the line of ANALYSE.cya from		If you do not have an access to parallel computation change the line of ANALYSE.cya from
	system "bsub python ~/~~Python~~/~~allosteryExtraction~~/correlationExtraction.py $dir/splitall.pdb --therm_iter=5"		system "bsub python '''PATH/To/PDBcor'''/correlationExtraction.py $dir/splitall.pdb --therm_iter=5"
	to:		to:
	system "python ~/~~Python~~/~~allosteryExtraction~~/correlationExtraction.py $dir/splitall.pdb --therm_iter=5"		system "python '''PATH/To/PDBcor'''/correlationExtraction.py $dir/splitall.pdb --therm_iter=5"

	Then, activate the PDBcor environment and run the correlation analysis:		Then, activate the PDBcor environment and run the correlation analysis:

Dima at 17:32, 6 September 2021

2021-09-06T17:32:22Z

← Older revision		Revision as of 19:32, 6 September 2021
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	Please follow the following steps carefully (exact Linux commands are given below; you may copy them to a terminal):		Please follow the following steps carefully (exact Linux commands are given below; you may copy them to a terminal):

	First, edit the protein specific data in the folder '''data/'''. Make sure, that filenames are kept the same as in the demo. Advanced users can ignore it and fix ~~PREP~~.cya for potential naming errors. Change the protein sequence in the root folder (same filename is not required).		First, edit the protein specific data in the folder '''data/'''. Make sure, that filenames are kept the same as in the demo. Advanced users can ignore it and fix PREPpop.cya for potential naming errors. Change the protein sequence in the root folder (same filename is not required).

	Additionally, do following checks:		Additionally, do following checks:

Dima at 17:31, 6 September 2021

2021-09-06T17:31:59Z

← Older revision		Revision as of 19:31, 6 September 2021
Line 25:		Line 25:
	Please follow the following steps carefully (exact Linux commands are given below; you may copy them to a terminal):		Please follow the following steps carefully (exact Linux commands are given below; you may copy them to a terminal):

	First, edit the protein specific data in the folder '''data/'''. Make sure, that filenames are kept the same as in the demo. Advanced users can ignore it and fix ~~PREPpop~~.cya for potential naming errors. Change the protein sequence in the root folder (same filename is not required).		First, edit the protein specific data in the folder '''data/'''. Make sure, that filenames are kept the same as in the demo. Advanced users can ignore it and fix PREP.cya for potential naming errors. Change the protein sequence in the root folder (same filename is not required).

	Additionally, do following checks:		Additionally, do following checks:

Dima: moved Determination of protein state populations to Determination of the protein state populations: Spelling

2021-09-06T17:29:44Z

moved Determination of protein state populations to Determination of the protein state populations: Spelling

← Older revision	Revision as of 19:29, 6 September 2021
(No difference)

Dima at 16:09, 6 September 2021

2021-09-06T16:09:44Z

← Older revision		Revision as of 18:09, 6 September 2021
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	In summary, our approach consists of following steps:		In summary, our approach consists of following steps:
	# We conduct a series of 10 state structure calculations with varying population parameter		# We conduct a series of 10-state structure calculations with varying population parameter
	# We evaluate structure calculations in terms of target function and correlations (using PDBcor)		# We evaluate structure calculations in terms of target function and correlations (using PDBcor)

Dima: Created page with "In this tutorial we will provide you with guided examples for determination of protein state populations. In summary, our approach consists of following steps: # We conduct ..."

2021-09-06T16:09:00Z

Created page with "In this tutorial we will provide you with guided examples for determination of protein state populations. In summary, our approach consists of following steps: # We conduct ..."

New page

In this tutorial we will provide you with guided examples for determination of protein state populations.

In summary, our approach consists of following steps:
# We conduct a series of 10 state structure calculations with varying population parameter
# We evaluate structure calculations in terms of target function and correlations (using PDBcor)

==== Software installation ====

This tutorial requires following software:
# CYANA
# Python3
# UCSF Chimera
# PDBcor. In case if PDBcor is not yet installed, please go to this [https://github.com/dzmitryashkinadze/PDBCor link] and follow installation instructions. Later we will refer to the PDBcor installation path as '''PATH/To/PDBcor'''

==== Data preparation ====

Please follow the following steps:
# Download the [[Media:Pop_demo.zip|demo data]].
# Unpack the demo data

==== Execution ====

We recommend to use parallel computation for the execution as it will significantly reduce the total running time.

Please follow the following steps carefully (exact Linux commands are given below; you may copy them to a terminal):

First, edit the protein specific data in the folder '''data/'''. Make sure, that filenames are kept the same as in the demo. Advanced users can ignore it and fix PREPpop.cya for potential naming errors. Change the protein sequence in the root folder (same filename is not required).

Additionally, do following checks:

Check that '''init.cya''' and '''CALC.cya''' have '''rmsdrange''' variable (range to calculate RMSD of the protein bundle) set to correct value

Check that '''SPLIT.cya''' has '''nres''' variable (number of residues) set to correct value

Then, test the '''data/''' folder by running a test calculation:
cp -r data test
cd test
cyana PREPpop.cya populations=5,5
cyana -n 20 CALC.cya '''#cyana CALC.cya if no parallel computing is available'''

Check that both PREP and CALC scripts run without errors.

Check in program Chimera that resulting structure '''bundle.pdb''' is correct.

Check that split structure '''splitall.pdb''' is split correct (each conformer 1-nres is a separate PDB model).

Then, edit RUN.cya:

Edit the cyana engine
cyana:=cyana (do it only if you are sure what it is)

If you do not have an access to parallel computation change the line of RUN.cya from
system "pwd; ls -l CALC.cya; $cyana -n 20 CALC inputseed=$seed"
to:
system "pwd; ls -l CALC.cya; $cyana CALC inputseed=$seed"

Then, run the series of two-state structure calculations:
cyana RUN.cya

This creates a folder for each 10-state structure calculation. Final structure is saved as bundle.pdb and final split structure (where each state is an independent model is saved as splitall.pdb).

If you do not have an access to parallel computation change the line of ANALYSE.cya from
system "bsub python ~/Python/allosteryExtraction/correlationExtraction.py $dir/splitall.pdb --therm_iter=5"
to:
system "python ~/Python/allosteryExtraction/correlationExtraction.py $dir/splitall.pdb --therm_iter=5"

Then, activate the PDBcor environment and run the correlation analysis:
source '''PATH/To/PDBcor'''/venv/bin/activate
cyana ANALYSE.cya

This creates a '''correlations/''' subfolder in each structure calculation folder with a correlation value that can be read from the '''correlations_backbone.txt''' file.

Finally, collect results in a single file:
cyana STAT_COLLECT.cya

This collects all correlation and target function values of all executed calculations in a single file using bash script '''extract_cor_value.sh''' into the output file '''results.txt'''.