Strukturrechnung mit CYANA (2010) - Revision history

imported>Guentert: moved Strukturrechnung mit CYANA to Strukturrechnung mit CYANA (2010)

2011-01-21T09:48:36Z

moved Strukturrechnung mit CYANA to Strukturrechnung mit CYANA (2010)

← Older revision	Revision as of 09:48, 21 January 2011
(No difference)

imported>Guentert at 15:05, 14 January 2010

2010-01-14T15:05:28Z

← Older revision		Revision as of 15:05, 14 January 2010
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	The '''read upl''' command reads the input file with upper distance limits, et1.upl.		The '''read upl''' command reads the input file with upper distance limits, et1.upl.

	<!--The '''ssbond''' command adds restraints for the disulfide bond between residues Cys1 and Cys6.-->		<!--The '''ssbond''' command adds restraints for the disulfide bond between residues Cys1 and Cys6.
			-->
	The '''calc_all''' command performs a structure calculation starting from 50 conformers with random torsion angle values. Simulated annealing with 3000 torsion angle dynamics steps per conformer is used.		The '''calc_all''' command performs a structure calculation starting from 50 conformers with random torsion angle values. Simulated annealing with 3000 torsion angle dynamics steps per conformer is used.

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	<!--		<!--
	=== Printing ===		== Printing ==

	A local printer can be accessed with the name '''bpc_lokal''' from Linux, or '''BPC HP Laser Jet 4250 PS''' from Windows XP.		A local printer can be accessed with the name '''bpc_lokal''' from Linux, or '''BPC HP Laser Jet 4250 PS''' from Windows XP.
	-->		-->

imported>Guentert at 15:04, 14 January 2010

2010-01-14T15:04:48Z

← Older revision		Revision as of 15:04, 14 January 2010
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	cd et1		cd et1

	=== Write the sequence file ===		== Write the sequence file ==

	Use a text editor to write a new file called '''et1.seq''' (e.g., using the command '''kate et1.seq''' on the Linux command line) that contains the Endothelin-1 sequence, one upper-case residue name per line, given in the standard three-letter code for amino acids (except for cysteine residues that are involved in a disulfide bond, which are denoted by "CYSS"), e.g.		Use a text editor to write a new file called '''et1.seq''' (e.g., using the command '''kate et1.seq''' on the Linux command line) that contains the Endothelin-1 sequence, one upper-case residue name per line, given in the standard three-letter code for amino acids (except for cysteine residues that are involved in a disulfide bond, which are denoted by "CYSS"), e.g.
Line 51:		Line 51:
	TRP		TRP

	=== Write the initialization script ===		== Write the initialization script ==

	Use a text editor to write a new initialization script, '''init.cya''', for the program CYANA with the following content:		Use a text editor to write a new initialization script, '''init.cya''', for the program CYANA with the following content:
Line 62:		Line 62:
	These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq et1.seq''' reads the polypeptide sequence. The command '''library rename H atom=HN''' changes the name of the backbone hydrogen atom from "H" to "HN". The variable '''rmsdrange''' is set to the preferred residue range for RMSD calculation.		These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq et1.seq''' reads the polypeptide sequence. The command '''library rename H atom=HN''' changes the name of the backbone hydrogen atom from "H" to "HN". The variable '''rmsdrange''' is set to the preferred residue range for RMSD calculation.

	=== Write the NOE distance restraint file ===		== Write the NOE distance restraint file ==

	Use a text editor to write a new file, '''et1.upl''', that contains the upper distance bounds derived from NOESY cross peaks, using the [http://www.cyana.org/wiki/index.php/Standard_CYANA_nomenclature standard CYANA nomenclature] for atoms in proteins and the same format as in the following example:		Use a text editor to write a new file, '''et1.upl''', that contains the upper distance bounds derived from NOESY cross peaks, using the [http://www.cyana.org/wiki/index.php/Standard_CYANA_nomenclature standard CYANA nomenclature] for atoms in proteins and the same format as in the following example:
Line 95:		Line 95:
	Degenerate groups of atoms, e.g. methyl groups, and diastereotopic pairs of hydrogen atoms, e.g. HB2/HB3 in serine, are referred to by "pseudoatoms" whose names are derived from the names of the hydrogen atoms that they represent by changing the first letter from "H" to "Q" and omitting the last digit. For instance, "HB2" and "HB3" are represented by a pseudoatom called "QB".		Degenerate groups of atoms, e.g. methyl groups, and diastereotopic pairs of hydrogen atoms, e.g. HB2/HB3 in serine, are referred to by "pseudoatoms" whose names are derived from the names of the hydrogen atoms that they represent by changing the first letter from "H" to "Q" and omitting the last digit. For instance, "HB2" and "HB3" are represented by a pseudoatom called "QB".

	=== Write the CYANA script to execute the structure calculation ===		== Write the CYANA script to execute the structure calculation ==

	Use a text editor to write a new CYANA script, '''CALC.cya''', with the following content:		Use a text editor to write a new CYANA script, '''CALC.cya''', with the following content:

	read upl et1.upl		read upl et1.upl
	ssbond 1-6		<!--ssbond 1-6-->
	calc_all 50 steps=3000		calc_all 50 steps=3000
	overview et1.ovw structures=10 pdb		overview et1.ovw structures=10 pdb
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	The '''read upl''' command reads the input file with upper distance limits, et1.upl.		The '''read upl''' command reads the input file with upper distance limits, et1.upl.

	The '''ssbond''' command adds restraints for the disulfide bond between residues Cys1 and Cys6.		<!--The '''ssbond''' command adds restraints for the disulfide bond between residues Cys1 and Cys6.-->

	The '''calc_all''' command performs a structure calculation starting from 50 conformers with random torsion angle values. Simulated annealing with 3000 torsion angle dynamics steps per conformer is used.		The '''calc_all''' command performs a structure calculation starting from 50 conformers with random torsion angle values. Simulated annealing with 3000 torsion angle dynamics steps per conformer is used.
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	The '''overview''' command sorts the resulting structures by ascending target function value, analyzes the 10 best conformers for violations of the conformational restraints, and saves the results of the analysis in an overview file, '''et1.ovw''', and the coordinates of the 10 best conformers in a PDB file, '''et1.pdb'''.		The '''overview''' command sorts the resulting structures by ascending target function value, analyzes the 10 best conformers for violations of the conformational restraints, and saves the results of the analysis in an overview file, '''et1.ovw''', and the coordinates of the 10 best conformers in a PDB file, '''et1.pdb'''.

	=== Run the CYANA structure calculation ===		== Run the CYANA structure calculation ==

	Start CYANA, and execute the CYANA script CALC.cya:		Start CYANA, and execute the CYANA script CALC.cya:
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	cyana> CALC		cyana> CALC

	=== Analyze the results of the structure calculation ===		== Analyze the results of the structure calculation ==

	The results of the structure calculation are the structural statistics in the overview file, et1.ovw, and the structure itself, which is represented by a bundle of 10 conformers whose coordinates are stored in the PDB file, et1.pdb.		The results of the structure calculation are the structural statistics in the overview file, et1.ovw, and the structure itself, which is represented by a bundle of 10 conformers whose coordinates are stored in the PDB file, et1.pdb.
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	The residue range used for the superposition is indicated. RMSD values are computed for the backbone and heavy atoms of the given residues. The average value, the standard deviation, and the minimal and maximal values of the RMSDs between the analyzed structures and their mean coordinates are calculated.		The residue range used for the superposition is indicated. RMSD values are computed for the backbone and heavy atoms of the given residues. The average value, the standard deviation, and the minimal and maximal values of the RMSDs between the analyzed structures and their mean coordinates are calculated.

	=== Visualize the structure ===		== Visualize the structure ==

	The program MOLMOL can visualize the bundle of conformers that represents the solution structure of the peptide. Use the command		The program MOLMOL can visualize the bundle of conformers that represents the solution structure of the peptide. Use the command

	molmol -r 1-6 et1.pdb		molmol -r 8-21 et1.pdb

	to start the program MOLMOL and to show a superposition of the 10 conformers whose coordinates are stored in the PDB file et1.pdb. The option "-r 1-6" indicates MOLMOL to optimally superimpose the backbone atoms of residues 1-6.		to start the program MOLMOL and to show a superposition of the 10 conformers whose coordinates are stored in the PDB file et1.pdb. The option "-r 8-21" indicates MOLMOL to optimally superimpose the backbone atoms of residues 8-21.

	<!--		<!--

imported>Guentert at 15:03, 14 January 2010

2010-01-14T15:03:08Z

← Older revision		Revision as of 15:03, 14 January 2010
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	=== Startup ===		== Startup ==

	Log in to the Windows XP system with the username and password of your HRZ account.		Log in to the Windows XP system with the username and password of your HRZ account.

imported>Guentert at 14:59, 14 January 2010

2010-01-14T14:59:21Z

← Older revision		Revision as of 14:59, 14 January 2010
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	. /usr/local/courseexchange/cyana_setup.sh		. /usr/local/courseexchange/cyana_setup.sh

	(Alternatively, you can [[media:cyana~~-3.0~~-et1.tgz\|download the CYANA software]] into your home directory, and execute the setup commands		(Alternatively, you can [[media:cyana-et1.tgz\|download the CYANA software]] into your home directory, and execute the setup commands

	cd		cd

imported>Guentert: /* Startup */

2010-01-14T08:06:04Z

Startup

← Older revision		Revision as of 08:06, 14 January 2010
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	in order to run the software on any of the Linux servers, blade41, blade49, blade4a, or blade4b.)		in order to run the software on any of the Linux servers, blade41, blade49, blade4a, or blade4b.)

	Create a new directory, '''et1''', for the structure calculation, and change into it:		Create a new directory, '''et1''', for the structure calculation, and change into it:

imported>Guentert: /* Startup */

2010-01-14T08:05:47Z

Startup

← Older revision		Revision as of 08:05, 14 January 2010
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	The structure calculation will be performed on a Linux server that can be accessed by clicking the icon labeled '''BCC Linux Terminal-Service.nxs'''. The username and password for the Linux server are the same as for the Windows XP computer, and the data in the home directories are shared between the two systems.		The structure calculation will be performed on a Linux server that can be accessed by clicking the icon labeled '''BCC Linux Terminal-Service.nxs'''. The username and password for the Linux server are the same as for the Windows XP computer, and the data in the home directories are shared between the two systems.

	In a terminal window, login to the 'blade41' server, start the bash shell and execute the setup ~~command~~		In a terminal window, login to the 'blade41' server, start the bash shell and execute the setup commands

	ssh -X blade41.rz.uni-frankfurt.de		ssh -X blade41.rz.uni-frankfurt.de
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	. /usr/local/courseexchange/cyana_setup.sh		. /usr/local/courseexchange/cyana_setup.sh

			(Alternatively, you can [[media:cyana-3.0-et1.tgz\|download the CYANA software]] into your home directory, and execute the setup commands

			cd
			bash
			tar zxf Cyana-3.0-et1.tgz
			. cyana-3.0/cyana_setup.sh

			in order to run the software on any of the Linux servers, blade41, blade49, blade4a, or blade4b.)
	Create a new directory, '''et1''', for the structure calculation, and change into it:		Create a new directory, '''et1''', for the structure calculation, and change into it:

imported>Guentert: /* Write the initialization script */

2010-01-13T22:48:36Z

Write the initialization script

← Older revision		Revision as of 22:48, 13 January 2010
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	read seq et1.seq		read seq et1.seq
	library rename H atom=HN		library rename H atom=HN
	rmsdrange:=1-6		rmsdrange:=1-16

	These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq et1.seq''' reads the polypeptide sequence. The command '''library rename H atom=HN''' changes the name of the backbone hydrogen atom from "H" to "HN". The variable '''rmsdrange''' is set to the preferred residue range for RMSD calculation.		These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq et1.seq''' reads the polypeptide sequence. The command '''library rename H atom=HN''' changes the name of the backbone hydrogen atom from "H" to "HN". The variable '''rmsdrange''' is set to the preferred residue range for RMSD calculation.

imported>Guentert at 22:47, 13 January 2010

2010-01-13T22:47:07Z

← Older revision		Revision as of 22:47, 13 January 2010
Line 5:		Line 5:
	The structure calculation will be performed on a Linux server that can be accessed by clicking the icon labeled '''BCC Linux Terminal-Service.nxs'''. The username and password for the Linux server are the same as for the Windows XP computer, and the data in the home directories are shared between the two systems.		The structure calculation will be performed on a Linux server that can be accessed by clicking the icon labeled '''BCC Linux Terminal-Service.nxs'''. The username and password for the Linux server are the same as for the Windows XP computer, and the data in the home directories are shared between the two systems.

	In a terminal window, start the bash shell and execute the setup command		In a terminal window, login to the 'blade41' server, start the bash shell and execute the setup command

			ssh -X blade41.rz.uni-frankfurt.de
	bash		bash
	. /usr/local/courseexchange/cyana_setup.sh		. /usr/local/courseexchange/cyana_setup.sh

imported>Guentert at 22:43, 13 January 2010

2010-01-13T22:43:28Z

← Older revision		Revision as of 22:43, 13 January 2010
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	. /usr/local/courseexchange/cyana_setup.sh		. /usr/local/courseexchange/cyana_setup.sh

	Create a new directory, '''~~vaso~~''', for the structure calculation, and change into it:		Create a new directory, '''et1''', for the structure calculation, and change into it:

	mkdir ~~vaso~~		mkdir et1
	cd ~~vaso~~		cd et1

	=== Write the sequence file ===		=== Write the sequence file ===

	Use a text editor to write a new file called '''~~vaso~~.seq''' (e.g., using the command '''kate ~~vaso~~.seq''' on the Linux command line) that contains the ~~peptide~~ sequence, one upper-case residue name per line, given in the standard three-letter code for amino acids (except for cysteine residues that are involved in a disulfide bond, which are denoted by "CYSS"), e.g.		Use a text editor to write a new file called '''et1.seq''' (e.g., using the command '''kate et1.seq''' on the Linux command line) that contains the Endothelin-1 sequence, one upper-case residue name per line, given in the standard three-letter code for amino acids (except for cysteine residues that are involved in a disulfide bond, which are denoted by "CYSS"), e.g.

	~~CYSS~~		ALA
			SER
			ALA
			SER
			SER
			LEU
			MET
			ASP
			LYS
			GLU
			ALA
			VAL
	TYR		TYR
	PHE		PHE
	~~GLN~~		ALA
	~~ASN~~		HIS
	~~CYSS~~		LEU
	~~PRO~~		ASP
	~~ARG~~		ILE
	~~GLY~~		ILE
			TRP

	=== Write the initialization script ===		=== Write the initialization script ===
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	cyanalib		cyanalib
	read seq ~~vaso~~.seq		read seq et1.seq
	library rename H atom=HN		library rename H atom=HN
	rmsdrange:=1-6		rmsdrange:=1-6

	These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq ~~vaso~~.seq''' reads the polypeptide sequence. The command '''library rename H atom=HN''' changes the name of the backbone hydrogen atom from "H" to "HN". The variable '''rmsdrange''' is set to the preferred residue range for RMSD calculation.		These two commands will be executed automatically whenever the program CYANA is started. The '''cyanalib''' command reads the standard residue library of CYANA, and the command '''read seq et1.seq''' reads the polypeptide sequence. The command '''library rename H atom=HN''' changes the name of the backbone hydrogen atom from "H" to "HN". The variable '''rmsdrange''' is set to the preferred residue range for RMSD calculation.

	=== Write the NOE distance restraint file ===		=== Write the NOE distance restraint file ===

	Use a text editor to write a new file, '''~~vaso~~.upl''', that contains the upper distance bounds derived from NOESY cross peaks, using the [http://www.cyana.org/wiki/index.php/Standard_CYANA_nomenclature standard CYANA nomenclature] for atoms in proteins and the same format as in the following example:		Use a text editor to write a new file, '''et1.upl''', that contains the upper distance bounds derived from NOESY cross peaks, using the [http://www.cyana.org/wiki/index.php/Standard_CYANA_nomenclature standard CYANA nomenclature] for atoms in proteins and the same format as in the following example:

	91 THR HB 93 GLN QB 5.50		91 THR HB 93 GLN QB 5.50
Line 77:		Line 89:
	Use a text editor to write a new CYANA script, '''CALC.cya''', with the following content:		Use a text editor to write a new CYANA script, '''CALC.cya''', with the following content:

	read upl ~~vaso~~.upl		read upl et1.upl
	ssbond 1-6		ssbond 1-6
	calc_all 50 steps=3000		calc_all 50 steps=3000
	overview ~~vaso~~.ovw structures=10 pdb		overview et1.ovw structures=10 pdb

	The '''read upl''' command reads the input file with upper distance limits, ~~vaso~~.upl.		The '''read upl''' command reads the input file with upper distance limits, et1.upl.

	The '''ssbond''' command adds restraints for the disulfide bond between residues Cys1 and Cys6.		The '''ssbond''' command adds restraints for the disulfide bond between residues Cys1 and Cys6.
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	The '''calc_all''' command performs a structure calculation starting from 50 conformers with random torsion angle values. Simulated annealing with 3000 torsion angle dynamics steps per conformer is used.		The '''calc_all''' command performs a structure calculation starting from 50 conformers with random torsion angle values. Simulated annealing with 3000 torsion angle dynamics steps per conformer is used.

	The '''overview''' command sorts the resulting structures by ascending target function value, analyzes the 10 best conformers for violations of the conformational restraints, and saves the results of the analysis in an overview file, '''~~vaso~~.ovw''', and the coordinates of the 10 best conformers in a PDB file, '''~~vaso~~.pdb'''.		The '''overview''' command sorts the resulting structures by ascending target function value, analyzes the 10 best conformers for violations of the conformational restraints, and saves the results of the analysis in an overview file, '''et1.ovw''', and the coordinates of the 10 best conformers in a PDB file, '''et1.pdb'''.

	=== Run the CYANA structure calculation ===		=== Run the CYANA structure calculation ===
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	=== Analyze the results of the structure calculation ===		=== Analyze the results of the structure calculation ===

	The results of the structure calculation are the structural statistics in the overview file, ~~vaso~~.ovw, and the structure itself, which is represented by a bundle of 10 conformers whose coordinates are stored in the PDB file, ~~vaso~~.pdb.		The results of the structure calculation are the structural statistics in the overview file, et1.ovw, and the structure itself, which is represented by a bundle of 10 conformers whose coordinates are stored in the PDB file, et1.pdb.

	The overview file, ~~vaso~~.ovw, has three parts. The file starts with a table of the target function values and restraint violation statistics. For example:		The overview file, et1.ovw, has three parts. The file starts with a table of the target function values and restraint violation statistics. For example:

	Structural statistics:		Structural statistics:
Line 168:		Line 180:
	The program MOLMOL can visualize the bundle of conformers that represents the solution structure of the peptide. Use the command		The program MOLMOL can visualize the bundle of conformers that represents the solution structure of the peptide. Use the command

	molmol -r 1-6 ~~vaso~~.pdb		molmol -r 1-6 et1.pdb

	to start the program MOLMOL and to show a superposition of the 10 conformers whose coordinates are stored in the PDB file ~~vaso~~.pdb. The option "-r 1-6" indicates MOLMOL to optimally superimpose the backbone atoms of residues 1-6.		to start the program MOLMOL and to show a superposition of the 10 conformers whose coordinates are stored in the PDB file et1.pdb. The option "-r 1-6" indicates MOLMOL to optimally superimpose the backbone atoms of residues 1-6.

			<!--
	=== Printing ===		=== Printing ===

	A local printer can be accessed with the name '''bpc_lokal''' from Linux, or '''BPC HP Laser Jet 4250 PS''' from Windows XP.		A local printer can be accessed with the name '''bpc_lokal''' from Linux, or '''BPC HP Laser Jet 4250 PS''' from Windows XP.
			-->