CYANA Structure Calculations Using AutoStructure - Revision history

Jma at 21:28, 6 January 2010

2010-01-06T21:28:47Z

← Older revision		Revision as of 21:28, 6 January 2010
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	== <span class="mw-headline"> '''References''' </span> ==		== <span class="mw-headline"> '''References''' </span> ==

	1.    Güntert, P,, Mumenthaler, C. and Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. ''J. Mol. Biol. 273'', 283-298.		[http://www.ncbi.nlm.nih.gov/pubmed/9367762?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2 1.    Güntert, P,, Mumenthaler, C. and Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. ''J. Mol. Biol. 273'', 283-298.]

	2.    Herrmann, T., Güntert P. and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.  ''J Mol Biol 319'', 209-227.<br>		[http://www.ncbi.nlm.nih.gov/pubmed/12051947?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=4 2.    Herrmann, T., Güntert P. and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.  ''J Mol Biol 319'', 209-227.]<br>

	3.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.		[http://www.ncbi.nlm.nih.gov/pubmed/16374783?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1 3.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.]

	<br>		<br> <br>
	<br>

Jma at 21:26, 6 January 2010

2010-01-06T21:26:17Z

← Older revision		Revision as of 21:26, 6 January 2010
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	== '''Introduction''' ==		== '''Introduction''' ==

	Here we describe the protocol used for performing CYANA ~~(Ref.~~ 1,2) structure calculations in each cycle of AutoStructure ~~(Ref.~~ 3).		Here we describe the protocol used for performing CYANA [1,2] structure calculations in each cycle of AutoStructure [3].

	== '''Protocol''' ==		== '''Protocol''' ==
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	<br>		<br>
			<br>
	<br>

	~~-- JimAramini - 07 Nov 2009~~

Yphuang at 21:06, 18 December 2009

2009-12-18T21:06:52Z

← Older revision		Revision as of 21:06, 18 December 2009
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	==== Figure 1:  AutoStructure Control File:  Command Section ====		==== Figure 1:  AutoStructure Control File:  Command Section ====

	[[Image:AScontrol CYANAcommand.png]]		[[Image:AScontrol CYANAcommand.png\|611x628px]]

	<br>		<br>

	Here is an example AutoStructure [[~~media~~:Controlfile_CYANArun.txt\|control file]] for a CYANA run.		Here is an example AutoStructure [[Media:Controlfile_CYANArun.txt\|control file]] for a CYANA run.

	== <span class="mw-headline">'''Starting a Calculation''' </span> ==		== <span class="mw-headline">'''Starting a Calculation''' </span> ==
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	<pre>/farm/software/AutoStructure/AutoStructure-2.2.1/bin/autostructure -c controlfile_CYANArun -o testCYANArun.out -v		<pre>/farm/software/AutoStructure/AutoStructure-2.2.1/bin/autostructure -c controlfile_CYANArun -o testCYANArun.out -v
	</pre>		</pre>
	<br>		<br>

	== <span class="mw-headline"> '''References''' </span> ==		== <span class="mw-headline"> '''References''' </span> ==

	1.    Güntert, P,, Mumenthaler, C. and Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. ''J. Mol. Biol. 273'', 283-298.		1.    Güntert, P,, Mumenthaler, C. and Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. ''J. Mol. Biol. 273'', 283-298.

	2.    Herrmann, T., Güntert P. and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.  ''J Mol Biol 319'', 209-227.<br>		2.    Herrmann, T., Güntert P. and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.  ''J Mol Biol 319'', 209-227.<br>

	3.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.		3.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.

Jma at 15:08, 8 November 2009

2009-11-08T15:08:35Z

← Older revision		Revision as of 15:08, 8 November 2009
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	== <span class="mw-headline"> '''References''' </span> ==		== <span class="mw-headline"> '''References''' </span> ==

	1. ~~<br>~~		1.    Güntert, P,, Mumenthaler, C. and Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. ''J. Mol. Biol. 273'', 283-298.

	2.		2.    Herrmann, T., Güntert P. and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.  ''J Mol Biol 319'', 209-227.<br>

	3.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.		3.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.

Jma at 15:03, 8 November 2009

2009-11-08T15:03:53Z

← Older revision		Revision as of 15:03, 8 November 2009
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	Here is an example AutoStructure [[media:Controlfile_CYANArun.txt\|control file]] for a CYANA run.		Here is an example AutoStructure [[media:Controlfile_CYANArun.txt\|control file]] for a CYANA run.

	== ~~<span class="editsection" />~~<span class="mw-headline">'''Starting a Calculation''' </span> ==		== <span class="mw-headline">'''Starting a Calculation''' </span> ==

	The AutoStructure run is best initiated from the command line in order to perform the structure calculations in parallel.  For example:		The AutoStructure run is best initiated from the command line in order to perform the structure calculations in parallel.  For example:
	<pre>/farm/software/AutoStructure/AutoStructure-2.2.1/bin/autostructure -c controlfile_CYANArun -o testCYANArun.out -v		<pre>/farm/software/AutoStructure/AutoStructure-2.2.1/bin/autostructure -c controlfile_CYANArun -o testCYANArun.out -v
	</pre>		</pre>
	<br>		<br>

	== <span class="mw-headline"> '''References''' </span> ==		== <span class="mw-headline"> '''References''' </span> ==

Jma at 14:58, 8 November 2009

2009-11-08T14:58:49Z

← Older revision		Revision as of 14:58, 8 November 2009
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	== '''Introduction''' ==		== '''Introduction''' ==

	Here we describe the protocol used for performing CYANA (Ref. 1,2) structure calculations in each cycle of AutoStructure (Ref. 3).		Here we describe the protocol used for performing CYANA (Ref. 1,2) structure calculations in each cycle of AutoStructure (Ref. 3).

	== '''Protocol''' ==		== '''Protocol''' ==

	The control file governs the options used in the execution of the AutoStructure run.  It is recommended that the user sets these options in the control file using the AutoStructure GUI.  The options are found in the Command ~~page~~ (Figure 1).  Select the CYANA-2.1 button.   The calculations are run over a cluster by a shell script called CreateProc.  Typically, we compute 100 structures per cycle (i.e., 4 structures in 25 nodes), and keep the best 20 structures (lowest target function) for input into the next round of NOESYASSIGN.  A queue system (i.e., PBS) is chosen for running over the cluster.  Additional files in CYANA format can be added to the structure calculation in this page, including dihedral angle constraints (.aco), hydrogen bond constraints and manual upper (.upl) and lower (.lol) distance constraints.		The control file governs the options used in the execution of the AutoStructure run.  It is recommended that the user sets these options in the control file using the AutoStructure GUI.  The options are found in the Command Section (Figure 1).  Select the CYANA-2.1 button.   The calculations are run over a cluster by a shell script called CreateProc.  Typically, we compute 100 structures per cycle (i.e., 4 structures in 25 nodes), and keep the best 20 structures (lowest target function) for input into the next round of NOESYASSIGN.  A queue system (i.e., PBS) is chosen for running over the cluster.  Additional files in CYANA format can be added to the structure calculation in this page, including dihedral angle constraints (.aco), hydrogen bond constraints and manual upper (.upl) and lower (.lol) distance constraints.

	==== Figure 1:  AutoStructure Control File:  Command ~~page~~ ====		==== Figure 1:  AutoStructure Control File:  Command Section ====

	[[Image:AScontrol CYANAcommand.png]]		[[Image:AScontrol CYANAcommand.png]]
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	<br>		<br>

	The ~~calculation~~ is best ~~run~~ from the command line in order to perform the structure calculations in parallel.  For example:		Here is an example AutoStructure [[media:Controlfile_CYANArun.txt\|control file]] for a CYANA run.

			== <span class="editsection" /><span class="mw-headline">'''Starting a Calculation''' </span> ==

			The AutoStructure run is best initiated from the command line in order to perform the structure calculations in parallel.  For example:
	<pre>/farm/software/AutoStructure/AutoStructure-2.2.1/bin/autostructure -c controlfile_CYANArun -o testCYANArun.out -v		<pre>/farm/software/AutoStructure/AutoStructure-2.2.1/bin/autostructure -c controlfile_CYANArun -o testCYANArun.out -v
	</pre>		</pre>
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	2.		2.

	3.		3.    Huang, Y.J., Tejero, R., Powers, R. and Montelione, G.T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data, ''Proteins 62'', 587-603.

	<br>		<br>
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	<br>		<br>

	-- JimAramini - 07 Nov 2009		-- JimAramini - 07 Nov 2009

Jma at 06:30, 8 November 2009

2009-11-08T06:30:43Z

← Older revision		Revision as of 06:30, 8 November 2009
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	2.		2.

			3.

	<br>		<br>

Jma at 06:27, 8 November 2009

2009-11-08T06:27:28Z

← Older revision		Revision as of 06:27, 8 November 2009
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	== '''Introduction''' ==		== '''Introduction''' ==

	Here we describe the protocol used for performing CYANA~~ ~~structure calculations in each cycle of AutoStructure.		Here we describe the protocol used for performing CYANA (Ref. 1,2) structure calculations in each cycle of AutoStructure (Ref. 3).

	== '''Protocol''' ==		== '''Protocol''' ==

Jma at 06:12, 8 November 2009

2009-11-08T06:12:11Z

← Older revision		Revision as of 06:12, 8 November 2009
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	The calculation is best run from the command line in order to perform the structure calculations in parallel.  For example:		The calculation is best run from the command line in order to perform the structure calculations in parallel.  For example:
	<pre>/farm/software/AutoStructure/AutoStructure-2.2.1/bin/autostructure -c controlfile_CYANArun -o testCYANArun.out -v		<pre>/farm/software/AutoStructure/AutoStructure-2.2.1/bin/autostructure -c controlfile_CYANArun -o testCYANArun.out -v
	</pre>		</pre>
			<br>

			== <span class="mw-headline"> '''References''' </span> ==
	== <span class="mw-headline"> '''References''' </span> ==

	1. <br>		1. <br>

Jma at 05:56, 8 November 2009

2009-11-08T05:56:39Z

← Older revision		Revision as of 05:56, 8 November 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	Here we describe the protocol used for performing CYANA structure calculations in each cycle of AutoStructure.		Here we describe the protocol used for performing CYANA structure calculations in each cycle of AutoStructure.

	== '''Protocol''' ==		== '''Protocol''' ==

	The control file governs the options used in the execution of the AutoStructure run.  It is recommended that the user sets these options in the control file using the AutoStructure GUI.  The options are found in the Command page (Figure 1).  Select the CYANA-2.1 button.   The calculations are run over a cluster by a shell script called CreateProc.  Typically, we compute 100 structures per cycle (i.e., 4 structures in 25 nodes), and keep the best 20 structures (lowest target function) for input into the next round of NOESYASSIGN.  A queue system (i.e., PBS) is chosen for running over the cluster.  Additional files in CYANA format can be added to the structure calculation in this page, including dihedral angle constraints (.aco), hydrogen bond constraints and manual upper (.upl) and lower (.lol) distance constraints.		The control file governs the options used in the execution of the AutoStructure run.  It is recommended that the user sets these options in the control file using the AutoStructure GUI.  The options are found in the Command page (Figure 1).  Select the CYANA-2.1 button.   The calculations are run over a cluster by a shell script called CreateProc.  Typically, we compute 100 structures per cycle (i.e., 4 structures in 25 nodes), and keep the best 20 structures (lowest target function) for input into the next round of NOESYASSIGN.  A queue system (i.e., PBS) is chosen for running over the cluster.  Additional files in CYANA format can be added to the structure calculation in this page, including dihedral angle constraints (.aco), hydrogen bond constraints and manual upper (.upl) and lower (.lol) distance constraints.

	==== Figure 1:  AutoStructure Control File:  Command page ====		==== Figure 1:  AutoStructure Control File:  Command page ====

	[[Image:~~AScontrol_CYANAcommand~~.png]]		[[Image:AScontrol CYANAcommand.png]]

			<br>

			The calculation is best run from the command line in order to perform the structure calculations in parallel.  For example:
			<pre>/farm/software/AutoStructure/AutoStructure-2.2.1/bin/autostructure -c controlfile_CYANArun -o testCYANArun.out -v
			</pre>

	~~The calculation is best run from the command line in order to perform the structure calculations in parallel.  For example:~~
	<~~pre~~>/~~farm/software/AutoStructure/AutoStructure-2~~.2.~~1/bin/autostructure~~ -~~c controlfile_CYANArun~~ -~~o testCYANArun.out~~ -~~v</pre>~~		== <span class="mw-headline"> '''References''' </span> ==

			1. <br>

			2.

			<br>

			<br>

			-- JimAramini - 07 Nov 2009