Automated resonance assignment with FLYA (EMBO 2015) - Revision history

Guentert: /* Automated NOESY assignment and structure calculation */

2015-08-03T11:29:00Z

Automated NOESY assignment and structure calculation

← Older revision		Revision as of 13:29, 3 August 2015
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	This will call the program TALOS+ and store the resulting torsion angle restraints in the file 'talos.aco'.		This will call the program TALOS+ and store the resulting torsion angle restraints in the file 'talos.aco'.

	For further information about automated NOESY assignment you can consult the Tutorial [[Structure calculation with automated NOESY assignment]].		For further information about automated NOESY assignment you can consult the Tutorial [[Structure calculation with automated NOESY assignment]] (which uses different file names than we have here).

	To speed up the calculation, you can set in 'CALC.cya':		To speed up the calculation, you can set in 'CALC.cya':

Guentert: /* Automated NOESY assignment and structure calculation */

2015-08-03T11:28:13Z

Automated NOESY assignment and structure calculation

← Older revision		Revision as of 13:28, 3 August 2015
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	This will call the program TALOS+ and store the resulting torsion angle restraints in the file 'talos.aco'.		This will call the program TALOS+ and store the resulting torsion angle restraints in the file 'talos.aco'.

			For further information about automated NOESY assignment you can consult the Tutorial [[Structure calculation with automated NOESY assignment]].

	To speed up the calculation, you can set in 'CALC.cya':		To speed up the calculation, you can set in 'CALC.cya':

Guentert at 09:54, 3 August 2015

2015-08-03T09:54:40Z

← Older revision		Revision as of 11:54, 3 August 2015
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	The 'flya.prot' file from the automated resonance assignment will be used together with the (unassigned) NOESY peak lists to assign the NOESY peaks and to generate distance restraints in order to compute the three-dimensional structure of the protein.		The 'flya.prot' file from the automated resonance assignment will be used together with the (unassigned) NOESY peak lists to assign the NOESY peaks and to generate distance restraints in order to compute the three-dimensional structure of the protein.

	To speed up the calculation, you can set in '~~CALC~~.cya' (above the 'flya' command):		To speed up the calculation, you can set in 'ASSIGN.cya' (above the 'flya' command):

	structures:=25,5		structures:=25,5

Guentert at 09:51, 3 August 2015

2015-08-03T09:51:53Z

← Older revision		Revision as of 11:51, 3 August 2015
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	== FLYA execution script ==		== FLYA execution script ==

	The CYANA script '~~CALC~~.cya' contains the commands to perform the automated resonance assignment. It starts with the specification of the names of the input peak lists:		The CYANA script 'ASSIGN.cya' contains the commands to perform the automated resonance assignment. It starts with the specification of the names of the input peak lists:

	structurepeaks:=N15NOESY,C13NOESY		structurepeaks:=N15NOESY,C13NOESY
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	== Run the FLYA calculation ==		== Run the FLYA calculation ==

	To run the FLYA calculation, you start CYANA and execute the '~~CALC~~.cya' script:		To run the FLYA calculation, you start CYANA and execute the 'ASSIGN.cya' script:

	cyana "nproc=2; ~~CALC~~"		cyana "nproc=2; ASSIGN"

	By specifying the 'nproc=2' command, the independent runs of the algorithm will be performed in parallel. On a computer with multiple processors this will speed up the calculation, which is expected to take a few minutes.		By specifying the 'nproc=2' command, the independent runs of the algorithm will be performed in parallel. On a computer with multiple processors this will speed up the calculation, which is expected to take a few minutes.
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	=== The flya.txt file ===		=== The flya.txt file ===

	This output file starts with overall assignment statistics for each group of atoms as defined by 'analyzeassign_group:=...' in ~~CALC~~.cya':		This output file starts with overall assignment statistics for each group of atoms as defined by 'analyzeassign_group:=...' in ASSIGN.cya':

	____________________________________________________________		____________________________________________________________
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	q		q

	The file 'fix.prot' will contain the reference chemical shifts only for the backbone (and CB) atoms H, N, CA, CB, C'. Now you can repeat the assignment calculation by inserting the 'shiftassign_fix:=fix.prot' statement in '~~CALC~~.cya' and choosing only the input peak lists that are relevant for sidechain assignment:		The file 'fix.prot' will contain the reference chemical shifts only for the backbone (and CB) atoms H, N, CA, CB, C'. Now you can repeat the assignment calculation by inserting the 'shiftassign_fix:=fix.prot' statement in 'ASSIGN.cya' and choosing only the input peak lists that are relevant for sidechain assignment:

	shiftassign_fix:=fix.prot		shiftassign_fix:=fix.prot
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	== Fully automated structure calculation ==		== Fully automated structure calculation ==

	Automated resonance assignment, automated NOE restraint assignment, and the structure calculation by torsion angle dynamics can be combined by running the 'flya' command in '~~CALC~~.cya' with the additional parameter 'stage=1':		Automated resonance assignment, automated NOE restraint assignment, and the structure calculation by torsion angle dynamics can be combined by running the 'flya' command in 'ASSIGN.cya' with the additional parameter 'stage=1':

	flya runs=10 shiftreference=ref.prot structurepeaks=$structurepeaks assignpeaks=$assignpeaks stage=1		flya runs=10 shiftreference=ref.prot structurepeaks=$structurepeaks assignpeaks=$assignpeaks stage=1

Guentert at 09:49, 3 August 2015

2015-08-03T09:49:05Z

← Older revision		Revision as of 11:49, 3 August 2015
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	In this tutorial we will determine the resonance assignments and the structure of a protein using the program CYANA.		In this tutorial we will determine the resonance assignments and the structure of a protein using the program CYANA.


	== CYANA setup for the EMBO Practical Course NMR in Munich (31 July - 7 August 2015) ==		== CYANA setup for the EMBO Practical Course NMR in Munich (31 July - 7 August 2015) ==
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	assignpeaks:=C13H1,N15H1,HCCH24,HCCH7,HBHACONH,C_CO_NH,HC_CO_NH		assignpeaks:=C13H1,N15H1,HCCH24,HCCH7,HBHACONH,C_CO_NH,HC_CO_NH

			<!--
	== Fully automated structure calculation ==		== Fully automated structure calculation ==

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	or with the [http://www.bpc.uni-frankfurt.de/cyrange.html CYRANGE web server].		or with the [http://www.bpc.uni-frankfurt.de/cyrange.html CYRANGE web server].
			-->
	== Automated NOESY assignment and structure calculation ==		== Automated NOESY assignment and structure calculation ==

Guentert at 09:47, 3 August 2015

2015-08-03T09:47:32Z

← Older revision		Revision as of 11:47, 3 August 2015
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	In this tutorial we will determine the resonance assignments and the structure of a protein using the program CYANA.		In this tutorial we will determine the resonance assignments and the structure of a protein using the program CYANA.


	== CYANA setup for the EMBO Practical Course NMR in Munich (31 July - 7 August 2015) ==		== CYANA setup for the EMBO Practical Course NMR in Munich (31 July - 7 August 2015) ==

Guentert at 09:46, 3 August 2015

2015-08-03T09:46:00Z

← Older revision		Revision as of 11:46, 3 August 2015
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	7 cycle of automated NOE assignment and structure calculation will be performed. Statistics on the NOE assignment and the structure calculation will be in the file 'Table', which can also be produced with the command 'cyanatable -lp'.		7 cycle of automated NOE assignment and structure calculation will be performed. Statistics on the NOE assignment and the structure calculation will be in the file 'Table', which can also be produced with the command 'cyanatable -lp'.

			The final structure will be 'final.pdb'. You can visualize it, for example, with the command

			molmol -r 8-110 final.pdb

			The optimal residue range for superposition can be found with the command

			cyana overlay final.pdb

			or with the [http://www.bpc.uni-frankfurt.de/cyrange.html CYRANGE web server].

			== Automated NOESY assignment and structure calculation ==

			Automated NOE restraint assignment and the structure calculation by torsion angle dynamics can be done with 'CALC.cya' macro. The 'flya.prot' file from the automated resonance assignment will be used together with the (unassigned) NOESY peak lists to assign the NOESY peaks and to generate distance restraints in order to compute the three-dimensional structure of the protein.

			TALOS+ can be used to generate torsion angle restraints from the backbone chemical shifts in 'flya.prot'. To do this, use the CYANA commands

			read flya.prot
			talos
			write talos.aco

			This will call the program TALOS+ and store the resulting torsion angle restraints in the file 'talos.aco'.

			To speed up the calculation, you can set in 'CALC.cya':

			structures:=50,10
			steps=5000

			These commands tell the program to calculate, in each cycle, 50 conformers, and to analyze the best 10 of them. 5000 torsion angle dynamics steps will be applied per conformer.

			7 cycle of automated NOE assignment and structure calculation will be performed by running the command

			cyana "nproc=2; CALC"

			Statistics on the NOE assignment and the structure calculation will be in the file 'Table', which can also be produced with the command 'cyanatable -lp'.

	The final structure will be 'final.pdb'. You can visualize it, for example, with the command		The final structure will be 'final.pdb'. You can visualize it, for example, with the command

Guentert: /* FLYA execution script */

2015-08-02T12:47:35Z

FLYA execution script

← Older revision		Revision as of 14:47, 2 August 2015
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	Experiments used for automated NOESY assignment and structure calculation are given in the 'structurepeaks:=...' statement (not relevant for the present practical); those for automated chemical shift assignment in the 'assignpeaks:=...' statement. The peak list names are separated by commas (without blanks!).		Experiments used for automated NOESY assignment and structure calculation are given in the 'structurepeaks:=...' statement (not relevant for the present practical); those for automated chemical shift assignment in the 'assignpeaks:=...' statement. The peak list names are separated by commas (without blanks!).

	The commands above will use all available peak lists. You can choose any subset of them by modifying the '~~noesy~~:=...' or '~~scalar~~:=...' statements.		The commands above will use all available peak lists. You can choose any subset of them by modifying the 'structurepeaks:=...' or 'assignpeaks:=...' statements.

	'''Try it!''' For instance, to make only backbone assignment using the <sup>15</sup>N-HSQC and triple resonance backbone assignment spectra, you can set		'''Try it!''' For instance, to make only backbone assignment using the <sup>15</sup>N-HSQC and triple resonance backbone assignment spectra, you can set

Guentert: /* The flya.txt file */

2015-07-29T07:51:40Z

The flya.txt file

← Older revision		Revision as of 09:51, 29 July 2015
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	* REFERENCES(2) is the number of reference assignments (in the selected group)		* REFERENCES(2) is the number of reference assignments (in the selected group)
	* CHEMICALSHIFTS(1) is is the number of atoms assigned by FLYA		* CHEMICALSHIFTS(1) is is the number of atoms assigned by FLYA
	* (1)and(2) is the number of atoms that are assigned by FLYA and in the reference ~~chemical shift list~~.		* (1)and(2) is the number of atoms that are assigned by FLYA and in the reference.
	* MATCH is the number of atoms with the same assignment by FLYA and in the reference. The percentage is relative to the number of reference assignments.		* MATCH is the number of atoms with the same assignment by FLYA and in the reference. The percentage is relative to the number of reference assignments.

Guentert: /* The flya.txt file */

2015-07-29T07:51:02Z

The flya.txt file

← Older revision		Revision as of 09:51, 29 July 2015
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	ALL: REFERENCES(2):1264 CHEMICALSHIFTS(1):1350 (1)and(2):1261 MATCH:1141(90.3% of (2))		ALL: REFERENCES(2):1264 CHEMICALSHIFTS(1):1350 (1)and(2):1261 MATCH:1141(90.3% of (2))


	* REFERENCES(2) is the number of reference assignments (in the selected group)		* REFERENCES(2) is the number of reference assignments (in the selected group)
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	* (1)and(2) is the number of atoms that are assigned by FLYA and in the reference chemical shift list.		* (1)and(2) is the number of atoms that are assigned by FLYA and in the reference chemical shift list.
	* MATCH is the number of atoms with the same assignment by FLYA and in the reference. The percentage is relative to the number of reference assignments.		* MATCH is the number of atoms with the same assignment by FLYA and in the reference. The percentage is relative to the number of reference assignments.


	Further below comes a table with information about each peak list:		Further below comes a table with information about each peak list: