Identification of key NOEs - Revision history

Dima: /* Execution */

2021-09-07T11:31:37Z

Execution

← Older revision		Revision as of 13:31, 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:

2021-09-06T16:05:43Z

← Older revision		Revision as of 18:05, 6 September 2021
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	# We extract all long range NOEs		# We extract all long range NOEs
	# For each long range NOE we run a two-state structure calculation missing this particular NOE		# For each long range NOE we run a two-state structure calculation missing this particular NOE
	# We evaluate structure calculations in terms of correlations (using PDBcor)		# We evaluate structure calculations in terms of target function and correlations (using PDBcor)

	==== Software installation ====		==== Software installation ====

2021-09-06T14:12:59Z

Execution

← Older revision		Revision as of 16:12, 6 September 2021
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	cyana ANALYSE.cya		cyana ANALYSE.cya

	This creates a '''~~correlation~~/''' subfolder in each structure calculation folder with a correlation value that can be read from the '''correlations_backbone.txt''' file.		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:		Finally, collect results in a single file:

2021-09-06T14:12:19Z

Execution

← Older revision		Revision as of 16:12, 6 September 2021
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	Additionally, do following checks:		Additionally, do following checks:

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

2021-09-06T14:07:34Z

Execution

← Older revision		Revision as of 16:07, 6 September 2021
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	cyana STAT_COLLECT.cya		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''' and then sorts them according to the target function ('''results_tf.txt''') and correlations ('''~~results_tf~~.txt''').		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''' and then sorts them according to the target function ('''results_tf.txt''') and correlations ('''results_cor.txt''').

2021-09-06T14:07:21Z

Execution

← Older revision		Revision as of 16:07, 6 September 2021
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	This creates a '''correlation/''' subfolder in each structure calculation folder with a correlation value that can be read from the '''correlations_backbone.txt''' file.		This creates a '''correlation/''' 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 ~~('''results.txt''')~~:		Finally, collect results in a single file:
	cyana STAT_COLLECT.cya		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'''.		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''' and then sorts them according to the target function ('''results_tf.txt''') and correlations ('''results_tf.txt''').

2021-09-06T13:53:59Z

← Older revision		Revision as of 15:53, 6 September 2021
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	# CYANA		# CYANA
	# Python3		# 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'''		# 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'''

2021-09-06T13:52:23Z

Execution

← Older revision		Revision as of 15:52, 6 September 2021
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	Then, edit RUN.cya:		Then, edit RUN.cya:

	Edit upl and lol filenames		Edit upl and lol filenames
	read upl data/demo.upl		read upl data/demo.upl
	read lol data/demo.lol		read lol data/demo.lol

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

2021-09-06T13:51:54Z

Execution

← Older revision		Revision as of 15:51, 6 September 2021
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	cyana -n 20 CALC.cya '''#cyana CALC.cya if no parallel computing is available'''		cyana -n 20 CALC.cya '''#cyana CALC.cya if no parallel computing is available'''

	If both PREP and CALC scripts run without errors ~~then proceed, otherwise fix errors~~.		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:		Then, edit RUN.cya:

2021-09-06T13:49:15Z

Execution

← Older revision		Revision as of 15:49, 6 September 2021
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	Additionally, do following checks:		Additionally, do following checks:

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

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