Strukturrechnung mit CYANA - Revision history

GuentertWiki at 14:18, 16 December 2019

2019-12-16T14:18:38Z

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	* Now change the directory using the command 'cd'. For our example:		* Now change the directory using the command 'cd'. For our example:
	cd Mueller		cd Mueller

	~~Download the tgz-archive file [[media:cyanadata0.tgz\|cyanadata.tgz]] with the input data for the CYANA structure calculations.~~

	In '''your group directory''', unpack the input data for the CYANA structure calculations:		In '''your group directory''', unpack the input data for the CYANA structure calculations:

GuentertWiki at 14:09, 16 December 2019

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	<!--Use either your own Windows laptop computer or log in to the Windows system with the username and password of your HRZ account.		<!--Use either your own Windows laptop computer or log in to the Windows system with the username and password of your HRZ account.
	-->		-->
	The structure calculation will be performed on a Linux server that can be accessed by a remote connection to our computer cluster. For the remote connection we use the program MobaXterm. This program provides a shell environment in Windows that allows us the access to the remote computer.		The structure calculation will be performed on a Linux server that can be accessed by a remote connection to our computer cluster. For the remote connection from a Windows computer, we use the program MobaXterm. This program provides a shell environment in Windows that allows us the access to the remote computer. (If you use a Mac or Linux laptop, please ask us.)
	To establish the connection to the server please follow the following steps:		To establish the connection to the server please follow the following steps:

GuentertWiki at 14:02, 16 December 2019

2019-12-16T14:02:09Z

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	The structure calculation with automated NOESY assignment ('manual-noeassign') can use the same peak list, but CYANA will not use the assignments, only the peak positions and volumes.		The structure calculation with automated NOESY assignment ('manual-noeassign') can use the same peak list, but CYANA will not use the assignments, only the peak positions and volumes.

	== ~~Run a~~ CYANA structure calculation with manually assigned data ==		== CYANA structure calculation with manually assigned data ==

	Start CYANA, and execute the CYANA script CALC.cya (in 'manual-manual'):		Start CYANA, and execute the CYANA script CALC.cya (in 'manual-manual'):
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	(Note that the jobs from all groups are run under the user name 'guest'. Check the directory name in the last column of the output to identify your job.)		(Note that the jobs from all groups are run under the user name 'guest'. Check the directory name in the last column of the output to identify your job.)

	== 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, sso7d.ovw ('manual-manual') or final.ovw ('manual-noeassign' and 'flya-noeassign'), and the structure itself, which is represented by a bundle of 10 conformers whose coordinates are stored in the PDB file, sso7d.pdb ('manual-manual') or final.pdb ('manual-noeassign' and 'flya-noeassign').		The results of the structure calculation are the structural statistics in the overview file, sso7d.ovw ('manual-manual') or final.ovw ('manual-noeassign' and 'flya-noeassign'), and the structure itself, which is represented by a bundle of 10 conformers whose coordinates are stored in the PDB file, sso7d.pdb ('manual-manual') or final.pdb ('manual-noeassign' and 'flya-noeassign').
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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 ===

	Look at the structure with a molecular viewer such as PyMol.		Look at the structure with a molecular viewer such as PyMol. The 'ref.pdb' file contains a "good" structure for comparison.

	== Structure calculation with automated NOESY peak assignment ==		== Structure calculation with automated NOESY peak assignment ==

GuentertWiki: /* Run a CYANA structure calculation with manually assigned data */

2019-12-16T14:00:45Z

Run a CYANA structure calculation with manually assigned data

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	cyana> CALC		cyana> CALC

	In this case, the structure calculation is performed in the terminal window and using a single processor. For the ~~following~~ structure calculations, it is more efficient and convenient to run them in batch mode on 50 processors in parallel with the command		In this case, the structure calculation is performed in the terminal window and using a single processor.

			For the subsequent structure calculations, it is more efficient and convenient to run them in batch mode on 50 processors in parallel with the command

	cyana -n 50 CALC		cyana -n 50 CALC

GuentertWiki at 13:59, 16 December 2019

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	The structure calculation with automated NOESY assignment ('manual-noeassign') can use the same peak list, but CYANA will not use the assignments, only the peak positions and volumes.		The structure calculation with automated NOESY assignment ('manual-noeassign') can use the same peak list, but CYANA will not use the assignments, only the peak positions and volumes.

	== Run ~~the~~ CYANA structure calculation ==		== Run a CYANA structure calculation with manually assigned data ==

	Start CYANA, and execute the CYANA script CALC.cya (in 'manual-manual'):		Start CYANA, and execute the CYANA script CALC.cya (in 'manual-manual'):
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	Sequence file "sso7d.seq" read, 65 residues.		Sequence file "sso7d.seq" read, 65 residues.
	cyana> CALC		cyana> CALC

			In this case, the structure calculation is performed in the terminal window and using a single processor. For the following structure calculations, it is more efficient and convenient to run them in batch mode on 50 processors in parallel with the command

			cyana -n 50 CALC

			You can monitor the status of your jobs with the command

			qa

			(Note that the jobs from all groups are run under the user name 'guest'. Check the directory name in the last column of the output to identify your job.)

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

GuentertWiki at 13:52, 16 December 2019

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	== Startup ==		== Startup ==

	Use either your own Windows laptop computer or log in to the Windows system with the username and password of your HRZ account.		<!--Use either your own Windows laptop computer or log in to the Windows system with the username and password of your HRZ account.
			-->
	The structure calculation will be performed on a Linux server that can be accessed by a remote connection to our computer cluster. For the remote connection we use the program MobaXterm. This program provides a shell environment in Windows that allows us the access to the remote computer.		The structure calculation will be performed on a Linux server that can be accessed by a remote connection to our computer cluster. For the remote connection we use the program MobaXterm. This program provides a shell environment in Windows that allows us the access to the remote computer.
	To establish the connection to the server please follow the following steps:		To establish the connection to the server please follow the following steps:

	* Copy the ZIP file [[Media:MobaXterm_v7.4.zip\|MobaXterm_v7.4.zip]] to you personal ~~folder~~ and unpack it.		* Copy the ZIP file [[Media:MobaXterm_v7.4.zip\|MobaXterm_v7.4.zip]] to you personal Windows computer and unpack it.
	* The folder contains two files, MobaXterm_Personal_7.4.exe (the program executable) and MobaXterm.ini an additional file containing all passwords and data necessary to automaticall access the server		* The folder contains two files, MobaXterm_Personal_7.4.exe (the program executable) and MobaXterm.ini an additional file containing all passwords and data necessary to automaticall access the server
	* Start the program by klicking the execuatble MobaXterm_Personal_7.4.exe.		* Start the program by klicking the execuatble MobaXterm_Personal_7.4.exe.

GuentertWiki: /* Structure calculation with automated NOESY peak assignment */

2019-12-16T13:42:20Z

Structure calculation with automated NOESY peak assignment

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	Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [http://www.cyana.org/wiki/index.php/Simulated_annealing simulated annealing] schedule with 10000 [http://www.cyana.org/wiki/index.php/Torsion_angle_dynamics torsion angle dynamics] steps per conformer. The 10 conformers with the lowest final target function values are analyzed. An [http://www.cyana.org/wiki/index.php/CYANA_Macro:_overview overview] table of these 10 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.		Seven cycles of combined automated NOESY assignment and structure calculation are performed, followed by a final structure calculation. In each cycle and in the final structure calculation 100 conformers are calculated using the standard [http://www.cyana.org/wiki/index.php/Simulated_annealing simulated annealing] schedule with 10000 [http://www.cyana.org/wiki/index.php/Torsion_angle_dynamics torsion angle dynamics] steps per conformer. The 10 conformers with the lowest final target function values are analyzed. An [http://www.cyana.org/wiki/index.php/CYANA_Macro:_overview overview] table of these 10 best conformers is saved in the file '''final.ovw''', and their coordinates are written to the PDB file '''final.pdb'''. The corresponding files from the intermediate cycles 1-7 are called '''cycle1.''', '''cycle2.''', etc.

	An overview table of the complete calculation can be obtained with the command [http://www.cyana.org/wiki/index.php/CYANA_script:_cyanatable ''cyanatable''] (at the Unix prompt) during or after the completion of the calculation.		An overview table of the complete calculation can be obtained with the command [http://www.cyana.org/wiki/index.php/CYANA_script:_cyanatable ''cyanatable -l''] (at the Unix prompt) during or after the completion of the calculation.

	== Structure calculation with automated chemical shift assignment and automated NOESY peak assignment ==		== Structure calculation with automated chemical shift assignment and automated NOESY peak assignment ==

GuentertWiki: /* Structure calculation with automated chemical shift assignment and automated NOESY peak assignment */

2019-12-16T13:40:21Z

Structure calculation with automated chemical shift assignment and automated NOESY peak assignment

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	;CALC.cya:CYANA script to run NOE assignment & structure calculation		;CALC.cya:CYANA script to run NOE assignment & structure calculation

	The contents of the flya.* output files are described [http://www.cyana.org/wiki/index.php/Automated_resonance_assignment_with_FLYA_(EMBO_2019)#FLYA_output_files here].		Automated chemical shift assignment uses, in addition to NOESY, through-bond spectra for backbone and side-chain assignment. The FLYA automated chemical shift assignment calculation is started with the command

			cyana -n 20 CALCFLYA

			The automatically determined chemical shift assignments are given in the 'flya.prot' output file. The contents of the other 'flya.*' output files are described [http://www.cyana.org/wiki/index.php/Automated_resonance_assignment_with_FLYA_(EMBO_2019)#FLYA_output_files here].

			Using the 'flya.prot' chemical shift list, a structure calculation with automated NOESY assignment can be started, as above, with the command

			cyana -n 50 CALC

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GuentertWiki: /* Structure calculation with automated chemical shift assignment and automated NOESY peak assignment */

2019-12-16T13:35:06Z

Structure calculation with automated chemical shift assignment and automated NOESY peak assignment

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	;ref.pdb:reference structure (for comparison only)		;ref.pdb:reference structure (for comparison only)
	;N15NOESY.peaks:peak list from 3D <sup>15</sup>N-resolved NOESY spectrum		;N15NOESY.peaks:peak list from 3D <sup>15</sup>N-resolved NOESY spectrum
	;*.peaks:peak lists from other spectra		;\*.peaks:peak lists from other spectra
	;CALCFLYA.cya:CYANA script to run chemical shift assignment (FLYA)		;CALCFLYA.cya:CYANA script to run chemical shift assignment (FLYA)
	;CALC.cya:CYANA script to run NOE assignment & structure calculation		;CALC.cya:CYANA script to run NOE assignment & structure calculation

	The contents of the flya.* output files are described [http://www.cyana.org/wiki/index.php/Automated_resonance_assignment_with_FLYA_(EMBO_2019)#FLYA_output_files\|here].		The contents of the flya.* output files are described [http://www.cyana.org/wiki/index.php/Automated_resonance_assignment_with_FLYA_(EMBO_2019)#FLYA_output_files here].

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GuentertWiki: /* Structure calculation with automated chemical shift assignment and automated NOESY peak assignment */

2019-12-16T13:33:49Z

Structure calculation with automated chemical shift assignment and automated NOESY peak assignment

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	;CALC.cya:CYANA script to run NOE assignment & structure calculation		;CALC.cya:CYANA script to run NOE assignment & structure calculation

	The contents of the flya.* output files are described [[http://www.cyana.org/wiki/index.php/Automated_resonance_assignment_with_FLYA_(EMBO_2019)#FLYA_output_files\|here]].		The contents of the flya.* output files are described [http://www.cyana.org/wiki/index.php/Automated_resonance_assignment_with_FLYA_(EMBO_2019)#FLYA_output_files\|here].

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