Automated NOESY Assignment Using CYANA - Revision history

Jma at 21:54, 6 January 2010

2010-01-06T21:54:57Z

← Older revision		Revision as of 21:54, 6 January 2010
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	The lowercase h denotes the indirect (NOE) <sup>1</sup>H dimension.		The lowercase h denotes the indirect (NOE) <sup>1</sup>H dimension.

	If your peaklist contains assigned peaks, then CYANA will be able to determine the peaklist dimensions based on these assignments.		If your peaklist contains assigned peaks, then CYANA will be able to determine the peaklist dimensions based on these assignments.

	== '''Running Automated Structure Calculation with CYANA 2.1''' ==		== '''Running Automated Structure Calculation with CYANA 2.1''' ==

	#Create a working subdirectory (for example, <tt>structure/cyana21/calc1</tt>).		#Create a working subdirectory (for example, <tt>structure/cyana21/calc1</tt>).
	#Create an init.cya file as described in [[CYANA\|Getting Started ]]or copy a previously used file. Set an appropriate RMSD calculation range.		#Create an init.cya file as described in [[CYANA\|Getting Started or]] copy a previously used file. Set an appropriate RMSD calculation range.
	#Copy the latest sequence (<tt>XXXX.seq</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. The sequence file and peaklist should in principle be the same as those used to [[FOUND\|run FOUND]].		#Copy the latest sequence (<tt>XXXX.seq</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. The sequence file and peaklist should in principle be the same as those used to [[FOUND\|run FOUND]].
	#Copy the updated atomlist (<tt>XXXX.prot</tt>). The spin labels in it should be swapped according to the [[FOUND\|output of FOUND]].		#Copy the updated atomlist (<tt>XXXX.prot</tt>). The spin labels in it should be swapped according to the [[FOUND\|output of FOUND]].
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	#Enter <tt>CALC</tt> at the cyana prompt.		#Enter <tt>CALC</tt> at the cyana prompt.

	<br>		<br>

	== '''Output files''' ==		== '''Output files''' ==
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	*<tt>#PBS -l walltime=02:00:00</tt> defines maximum allocated job execution time. The limit for the <tt>shorts_c</tt> queue is 2 hours, but even the most demanding CYANA job finish in less than one hour.		*<tt>#PBS -l walltime=02:00:00</tt> defines maximum allocated job execution time. The limit for the <tt>shorts_c</tt> queue is 2 hours, but even the most demanding CYANA job finish in less than one hour.

	<br> ~~-- Alex Eletksi - 12 Dec 2007~~		<br><br>

	~~-- Edited by JimAramini - Nov 2009~~

	<br>

	*[[Media:CALC_noeassign.cya\|CALC.cya]]: CYANA 2.1 automated structure calculation script		*[[Media:CALC_noeassign.cya\|CALC.cya]]: CYANA 2.1 automated structure calculation script

Jma at 16:50, 13 November 2009

2009-11-13T16:50:19Z

← Older revision		Revision as of 16:50, 13 November 2009
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	#Create a working subdirectory (for example, <tt>structure/cyana21/calc1</tt>).		#Create a working subdirectory (for example, <tt>structure/cyana21/calc1</tt>).
	#Create an init.cya file as described in "[[~~NESG:CYANAInitFile~~\|~~Creating an init.cya file for CYANA 2.1~~]]" or copy a previously used file. Set an appropriate RMSD calculation range.		#Create an init.cya file as described in [[CYANA\|Getting Started ]]or copy a previously used file. Set an appropriate RMSD calculation range.
	#Copy the latest sequence (<tt>XXXX.seq</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. The sequence file and peaklist should in principle be the same as those used to [[FOUND\|run FOUND]].		#Copy the latest sequence (<tt>XXXX.seq</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. The sequence file and peaklist should in principle be the same as those used to [[FOUND\|run FOUND]].
	#Copy the updated atomlist (<tt>XXXX.prot</tt>). The spin labels in it should be swapped according to the [[FOUND\|output of FOUND]].		#Copy the updated atomlist (<tt>XXXX.prot</tt>). The spin labels in it should be swapped according to the [[FOUND\|output of FOUND]].
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	#Enter <tt>CALC</tt> at the cyana prompt.		#Enter <tt>CALC</tt> at the cyana prompt.

	<br>		<br>

	== '''Output files''' ==		== '''Output files''' ==

Jma at 16:47, 13 November 2009

2009-11-13T16:47:06Z

← Older revision		Revision as of 16:47, 13 November 2009
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	If you are using completely unassigned peaklist (for example, picke from scratch in CARA), then you will need to add the following line to the peaklist header:		If you are using completely unassigned peaklist (for example, picke from scratch in CARA), then you will need to add the following line to the peaklist header:
	<pre>~~<tt>~~#CYANAFORMAT HNh~~</tt>~~</pre>		<pre>#CYANAFORMAT HNh</pre>
	or		or
	<pre>~~<tt>~~#CYANAFORMAT HCh~~</tt>~~</pre>		<pre>#CYANAFORMAT HCh</pre>
	The lowercase h denotes the indirect (NOE) <sup>1</sup>H dimension.		The lowercase h denotes the indirect (NOE) <sup>1</sup>H dimension.

	If your peaklist contains assigned peaks, then CYANA will be able to determine the peaklist dimensions based on these assignments.		If your peaklist contains assigned peaks, then CYANA will be able to determine the peaklist dimensions based on these assignments.

	== '''Running Automated Structure Calculation with CYANA 2.1''' ==		== '''Running Automated Structure Calculation with CYANA 2.1''' ==

Jma at 16:44, 13 November 2009

2009-11-13T16:44:59Z

← Older revision		Revision as of 16:44, 13 November 2009
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	= '''~~Automated NOE Assign CYANA Run~~''' =		== '''Introduction''' ==

	Below is the description of how to run CYANA 2.1 for automated NOE assignment if you are working with CARA.  A tutorial for performing structure calculations with automated NOESY assignments using CYANA 3.0 is available [http://www.cyana.org/wiki/index.php/Structure_calculation_with_automated_NOESY_assignment on-line].		Below is the description of how to run CYANA 2.1 for automated NOE assignment if you are working with CARA.  A tutorial for performing structure calculations with automated NOESY assignments using CYANA 3.0 is available [http://www.cyana.org/wiki/index.php/Structure_calculation_with_automated_NOESY_assignment on-line].

Jma at 16:44, 13 November 2009

2009-11-13T16:44:22Z

← Older revision		Revision as of 16:44, 13 November 2009
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	= '''Automated NOE Assign CYANA Run''' =		= '''Automated NOE Assign CYANA Run''' =

	Below is the description of how to run CYANA 2.1 for automated NOE assignment if you are working with CARA.		Below is the description of how to run CYANA 2.1 for automated NOE assignment if you are working with CARA.  A tutorial for performing structure calculations with automated NOESY assignments using CYANA 3.0 is available [http://www.cyana.org/wiki/index.php/Structure_calculation_with_automated_NOESY_assignment on-line].

	== '''Input files''' ==		== '''Input files''' ==
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	#If you used FOUND, then copy the <tt>gridsearch.aco</tt> file from the previous FOUND run.		#If you used FOUND, then copy the <tt>gridsearch.aco</tt> file from the previous FOUND run.
	#If you used FOUND, then copy the <tt>stereofound.cya</tt> file from the previous FOUND run. Make sure that incorrect stereospecific assignments have been commented out or removed.		#If you used FOUND, then copy the <tt>stereofound.cya</tt> file from the previous FOUND run. Make sure that incorrect stereospecific assignments have been commented out or removed.
	#(Optional) Generate the short-range UPL (<tt>short.upl</tt>) file based on the existing peak assignments. This is more convenient to do on a workstation. You can use the [[Media:~~make_short~~.cya\|make_short.cya]] script (see below). Alternatively, you can define a <tt>KEEP</tt> subroutine in the <tt>CALC.cya</tt> file.		#(Optional) Generate the short-range UPL (<tt>short.upl</tt>) file based on the existing peak assignments. This is more convenient to do on a workstation. You can use the [[Media:Make_short.cya\|make_short.cya]] script (see below). Alternatively, you can define a <tt>KEEP</tt> subroutine in the <tt>CALC.cya</tt> file.
	#Download the [[Media:CALC_noeassign.cya\|CALC.cya]] script (see below) and modify it according to the input data.		#Download the [[Media:CALC_noeassign.cya\|CALC.cya]] script (see below) and modify it according to the input data.

Jma: moved NoeassignCYANARun to Automated NOESY Assignment Using CYANA

2009-11-05T22:18:42Z

moved NoeassignCYANARun to Automated NOESY Assignment Using CYANA

← Older revision	Revision as of 22:18, 5 November 2009
(No difference)

Jma at 19:08, 4 November 2009

2009-11-04T19:08:18Z

Jma at 19:06, 4 November 2009

2009-11-04T19:06:33Z

Jma at 17:42, 4 November 2009

2009-11-04T17:42:54Z

← Older revision		Revision as of 17:42, 4 November 2009
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	<br> -- Alex Eletksi - 12 Dec 2007		<br> -- Alex Eletksi - 12 Dec 2007

			-- Edited by JimAramini - Nov 2009



	*[[NESG:%ATTACHURL%/CALC.cya\|CALC.cya]]: CYANA 2.1 automated structure calculation script		*[[NESG:%ATTACHURL%/CALC.cya\|CALC.cya]]: CYANA 2.1 automated structure calculation script

Jma at 19:08, 3 November 2009

2009-11-03T19:08:15Z

← Older revision		Revision as of 19:08, 3 November 2009
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	Use the subroutine <tt>KEEP</tt> to keep assignment for peaks that you are confident, which is helpful if you peak list contains simulated peaks for short range NOEs.		Use the subroutine <tt>KEEP</tt> to keep assignment for peaks that you are confident, which is helpful if you peak list contains simulated peaks for short range NOEs.

	==== '''cyana.pbs - PBS queue submission script''' ====		=== '''cyana.pbs - PBS queue submission script''' ===
	<pre>#!/bin/csh		<pre>#!/bin/csh
	#!/bin/csh		#!/bin/csh

← Older revision		Revision as of 19:08, 4 November 2009
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	#If you used FOUND, then copy the <tt>gridsearch.aco</tt> file from the previous FOUND run.		#If you used FOUND, then copy the <tt>gridsearch.aco</tt> file from the previous FOUND run.
	#If you used FOUND, then copy the <tt>stereofound.cya</tt> file from the previous FOUND run. Make sure that incorrect stereospecific assignments have been commented out or removed.		#If you used FOUND, then copy the <tt>stereofound.cya</tt> file from the previous FOUND run. Make sure that incorrect stereospecific assignments have been commented out or removed.
	#(Optional) Generate the short-range UPL (<tt>short.upl</tt>) file based on the existing peak assignments. This is more convenient to do on a workstation. You can use the [[~~media~~:~~short~~.cya\|make_short.cya]] script (see below). Alternatively, you can define a <tt>KEEP</tt> subroutine in the <tt>CALC.cya</tt> file.		#(Optional) Generate the short-range UPL (<tt>short.upl</tt>) file based on the existing peak assignments. This is more convenient to do on a workstation. You can use the [[Media:make_short.cya\|make_short.cya]] script (see below). Alternatively, you can define a <tt>KEEP</tt> subroutine in the <tt>CALC.cya</tt> file.
	#Download the [[~~media~~:CALC_noeassign.cya\|CALC.cya]] script (see below) and modify it according to the input data.		#Download the [[Media:CALC_noeassign.cya\|CALC.cya]] script (see below) and modify it according to the input data.

	You can choose whether you want to run structure calculation on a local Linux workstation or on the U2 Linux cluster. The typical machine times on a single workstation are 1.5 - 3 hours, depending on the protein size. Calculations on the cluster take only 15-30 minutes, but there my be additional queue waiting time. On weekdays during working hours (9 a.m. - 4 p.m.) there are 10 dual-processor nodes reserved for us only, and there is no waiting time.		You can choose whether you want to run structure calculation on a local Linux workstation or on the U2 Linux cluster. The typical machine times on a single workstation are 1.5 - 3 hours, depending on the protein size. Calculations on the cluster take only 15-30 minutes, but there my be additional queue waiting time. On weekdays during working hours (9 a.m. - 4 p.m.) there are 10 dual-processor nodes reserved for us only, and there is no waiting time.
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	#Create a working subdirectory (like <tt>username/XXXX/cyana21</tt>)		#Create a working subdirectory (like <tt>username/XXXX/cyana21</tt>)
	#Copy the entire subdirectory <tt>calc1</tt>. You can use <tt>gftp</tt>, <tt>scp</tt> or <tt>sftp</tt>.		#Copy the entire subdirectory <tt>calc1</tt>. You can use <tt>gftp</tt>, <tt>scp</tt> or <tt>sftp</tt>.
	#Download the PBS submission script [[~~media~~:~~cyana~~.pbs\|cyana.pbs]] (see below). Modify it if needed.		#Download the PBS submission script [[Media:Cyana.pbs\|cyana.pbs]] (see below). Modify it if needed.
	#Type <tt>qsub cyana.pbs</tt> to submit you job.		#Type <tt>qsub cyana.pbs</tt> to submit you job.

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	<br>		<br>

	*[[~~media~~:CALC_noeassign.cya\|CALC.cya]]: CYANA 2.1 automated structure calculation script		*[[Media:CALC_noeassign.cya\|CALC.cya]]: CYANA 2.1 automated structure calculation script

	*[[~~media~~:~~cyana~~.pbs\|cyana.pbs]]: PBS queue submission script for CYANA 2.1 on U2 cluster		*[[Media:Cyana.pbs\|cyana.pbs]]: PBS queue submission script for CYANA 2.1 on U2 cluster

	*[[~~media~~:~~make short~~.cya\|make_short.cya]]: CYANA script to run manual calculation with local constraints		*[[Media:Make_short.cya\|make_short.cya]]: CYANA script to run manual calculation with local constraints

← Older revision		Revision as of 19:06, 4 November 2009
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	*SequenceList in XEASY format - usually <tt>XXXX.seq</tt>, where XXXX is the NESG ID.		*SequenceList in XEASY format - usually <tt>XXXX.seq</tt>, where XXXX is the NESG ID.
	*AtomList in XEASY format <tt>XXXX.prot</tt> . Chemical shifts should be real, not folded. Make sure that you are using the most recent file. Atom labels should be swapped if using stereospecific assignments.		*AtomList in XEASY format <tt>XXXX.prot</tt> . Chemical shifts should be real, not folded. Make sure that you are using the most recent file. Atom labels should be swapped if using stereospecific assignments.
	*Separate unfolded PeakList for ~~15N~~ and ~~13C~~ NOESY: <tt>n.peaks</tt>, <tt>ali.peaks</tt>, <tt>aro.peaks</tt>.		*Separate unfolded PeakList for <sup>15</sup>N and <sup>13</sup>C NOESY: <tt>n.peaks</tt>, <tt>ali.peaks</tt>, <tt>aro.peaks</tt>.

	Optional files		Optional files
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	#If you used FOUND, then copy the <tt>gridsearch.aco</tt> file from the previous FOUND run.		#If you used FOUND, then copy the <tt>gridsearch.aco</tt> file from the previous FOUND run.
	#If you used FOUND, then copy the <tt>stereofound.cya</tt> file from the previous FOUND run. Make sure that incorrect stereospecific assignments have been commented out or removed.		#If you used FOUND, then copy the <tt>stereofound.cya</tt> file from the previous FOUND run. Make sure that incorrect stereospecific assignments have been commented out or removed.
	#(Optional) Generate the short-range UPL (<tt>short.upl</tt>) file based on the existing peak assignments. This is more convenient to do on a workstation. You can use the [[~~NESG~~:~~%ATTACHURL%/make~~ short.cya\|make_short.cya]] script (see below). Alternatively, you can define a <tt>KEEP</tt> subroutine in the <tt>CALC.cya</tt> file.		#(Optional) Generate the short-range UPL (<tt>short.upl</tt>) file based on the existing peak assignments. This is more convenient to do on a workstation. You can use the [[media:short.cya\|make_short.cya]] script (see below). Alternatively, you can define a <tt>KEEP</tt> subroutine in the <tt>CALC.cya</tt> file.
	#Download the [[~~NESG~~:~~%ATTACHURL%/CALC~~.cya\|CALC.cya]] script (see below) and modify it according to the input data.		#Download the [[media:CALC_noeassign.cya\|CALC.cya]] script (see below) and modify it according to the input data.

	You can choose whether you want to run structure calculation on a local Linux workstation or on the U2 Linux cluster. The typical machine times on a single workstation are 1.5 - 3 hours, depending on the protein size. Calculations on the cluster take only 15-30 minutes, but there my be additional queue waiting time. On weekdays during working hours (9 a.m. - 4 p.m.) there are 10 dual-processor nodes reserved for us only, and there is no waiting time.		You can choose whether you want to run structure calculation on a local Linux workstation or on the U2 Linux cluster. The typical machine times on a single workstation are 1.5 - 3 hours, depending on the protein size. Calculations on the cluster take only 15-30 minutes, but there my be additional queue waiting time. On weekdays during working hours (9 a.m. - 4 p.m.) there are 10 dual-processor nodes reserved for us only, and there is no waiting time.
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	#Create a working subdirectory (like <tt>username/XXXX/cyana21</tt>)		#Create a working subdirectory (like <tt>username/XXXX/cyana21</tt>)
	#Copy the entire subdirectory <tt>calc1</tt>. You can use <tt>gftp</tt>, <tt>scp</tt> or <tt>sftp</tt>.		#Copy the entire subdirectory <tt>calc1</tt>. You can use <tt>gftp</tt>, <tt>scp</tt> or <tt>sftp</tt>.
	#Download the PBS submission script [[~~NESG~~:~~%ATTACHURL%/~~cyana.pbs\|cyana.pbs]] (see below). Modify it if needed.		#Download the PBS submission script [[media:cyana.pbs\|cyana.pbs]] (see below). Modify it if needed.
	#Type <tt>qsub cyana.pbs</tt> to submit you job.		#Type <tt>qsub cyana.pbs</tt> to submit you job.

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	<br> For the <tt>calibration</tt> parameter you can provide the list of calibration constants you have derived for the "backbone" class with <tt>caliba</tt>, when you calibrated the initial peak lists for use with FOUND/HABAS. Do not comment or delete this line, leave it blank if you want automatic calibration. Automatic calibration uses the <tt>dref</tt> parameter as the presumed average distance for all peaks in a peaklist (not just for backbone, like <tt>caliba</tt>).<br>		<br> For the <tt>calibration</tt> parameter you can provide the list of calibration constants you have derived for the "backbone" class with <tt>caliba</tt>, when you calibrated the initial peak lists for use with FOUND/HABAS. Do not comment or delete this line, leave it blank if you want automatic calibration. Automatic calibration uses the <tt>dref</tt> parameter as the presumed average distance for all peaks in a peaklist (not just for backbone, like <tt>caliba</tt>).<br>

	<br>		<br>

	=== '''CALC.cya''' ===		=== '''CALC.cya''' ===
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	Use the <tt>protocol</tt> keywords to enable output logging when running CYANA on a workstation. They may not be necessary on a cluster, because the queue system generates its own log.		Use the <tt>protocol</tt> keywords to enable output logging when running CYANA on a workstation. They may not be necessary on a cluster, because the queue system generates its own log.

	Use the subroutine <tt>KEEP</tt> to keep assignment for peaks that you are confident, which is helpful if you peak list contains simulated peaks for short range NOEs.		Use the subroutine <tt>KEEP</tt> to keep assignment for peaks that you are confident, which is helpful if you peak list contains simulated peaks for short range NOEs.

	=== '''cyana.pbs - PBS queue submission script''' ===		=== '''cyana.pbs - PBS queue submission script''' ===
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	<br> -- Alex Eletksi - 12 Dec 2007		<br> -- Alex Eletksi - 12 Dec 2007

	-- Edited by JimAramini - Nov 2009		-- Edited by JimAramini - Nov 2009


			<br>

	*[[~~NESG~~:~~%ATTACHURL%/CALC~~.cya\|CALC.cya]]: CYANA 2.1 automated structure calculation script		*[[media:CALC_noeassign.cya\|CALC.cya]]: CYANA 2.1 automated structure calculation script

	*[[~~NESG~~:~~%ATTACHURL%/~~cyana.pbs\|cyana.pbs]]: PBS queue submission script for CYANA 2.1 on U2 cluster		*[[media:cyana.pbs\|cyana.pbs]]: PBS queue submission script for CYANA 2.1 on U2 cluster

	*[[~~NESG~~:~~%ATTACHURL%/~~make short.cya\|make_short.cya]]: CYANA script to run manual calculation with local constraints		*[[media:make short.cya\|make_short.cya]]: CYANA script to run manual calculation with local constraints