Manual Structure Calculation Using CYANA - Revision history

Jma at 21:54, 6 January 2010

2010-01-06T21:54:13Z

← Older revision		Revision as of 21:54, 6 January 2010
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	== '''Introduction''' ==		== '''Introduction''' ==

	Here we describe structure calcuation with manual NOE asignments using CYANA 2.1.  A tutorial is also avaliable [http://www.cyana.org/wiki/index.php/Structure_calculation_using_manually_assigned_NOESY_peak_lists on-line] for manual structure calculation using CYANA 3.0.		Here we describe structure calcuation with manual NOE asignments using CYANA 2.1.  A tutorial is also avaliable [http://www.cyana.org/wiki/index.php/Structure_calculation_using_manually_assigned_NOESY_peak_lists on-line] for manual structure calculation using CYANA 3.0.

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

	Manual structure calculation is performed similar to the [[NoeassignCYANARun\|automated calculation]].		Manual structure calculation is performed similar to the [[NoeassignCYANARun\|automated calculation]].
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	Macro <tt>peakcheck</tt> verifies AtomList and peaklists for consistency and is very useful when manually assigned peaks are used.		Macro <tt>peakcheck</tt> verifies AtomList and peaklists for consistency and is very useful when manually assigned peaks are used.

	It is important to set peak volumes to their absolute values before calling caliba for calibration.		It is important to set peak volumes to their absolute values before calling caliba for calibration.

	~~<br>~~

	~~-- AlexEletski - 10 Jul 2007~~

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

Jma at 16:54, 13 November 2009

2009-11-13T16:54:46Z

← Older revision		Revision as of 16:54, 13 November 2009
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	= '''~~Manual structure calculation with CYANA 2.1~~''' =		== '''Introduction''' ==

	== '''~~Introduction~~''' ==		Here we describe structure calcuation with manual NOE asignments using CYANA 2.1.  A tutorial is also avaliable [http://www.cyana.org/wiki/index.php/Structure_calculation_using_manually_assigned_NOESY_peak_lists on-line] for manual structure calculation using CYANA 3.0.

			== '''Protocol''' ==

	Manual structure calculation is performed similar to the [[NoeassignCYANARun\|automated calculation]].		Manual structure calculation is performed similar to the [[NoeassignCYANARun\|automated calculation]].
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	#Copy the latest <tt>stereofound.cya</tt> from the latest GridSearch run.		#Copy the latest <tt>stereofound.cya</tt> from the latest GridSearch run.
	#(Optional) Copy the <tt>talos.aco</tt> file		#(Optional) Copy the <tt>talos.aco</tt> file
	#Download the [[~~media~~:CALC_manual.cya\|CALC.cya]] file (see below). Modify peaklist names, calibration parameters and tolerances.		#Download the [[Media:CALC_manual.cya\|CALC.cya]] file (see below). Modify peaklist names, calibration parameters and tolerances.
	#Run calculation with CYANA 2.1 on a workstation or U2 cluster		#Run calculation with CYANA 2.1 on a workstation or U2 cluster

Jma: moved ManualCYANARun to Manual Structure Calculation Using CYANA

2009-11-05T22:20:05Z

moved ManualCYANARun to Manual Structure Calculation Using CYANA

← Older revision	Revision as of 22:20, 5 November 2009
(No difference)

Jma at 19:01, 4 November 2009

2009-11-04T19:01:57Z

← Older revision		Revision as of 19:01, 4 November 2009
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	= '''Manual structure calculation with CYANA 2.1''' =		= '''Manual structure calculation with CYANA 2.1''' =

	== '''Introduction''' ==		== '''Introduction''' ==
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	#Copy the latest <tt>stereofound.cya</tt> from the latest GridSearch run.		#Copy the latest <tt>stereofound.cya</tt> from the latest GridSearch run.
	#(Optional) Copy the <tt>talos.aco</tt> file		#(Optional) Copy the <tt>talos.aco</tt> file
	#Download the [[~~NESG~~:~~%ATTACHURL%/CALC~~.cya\|CALC.cya]] file (see below). Modify peaklist names, calibration parameters and tolerances.		#Download the [[media:CALC_manual.cya\|CALC.cya]] file (see below). Modify peaklist names, calibration parameters and tolerances.
	#Run calculation with CYANA 2.1 on a workstation or U2 cluster		#Run calculation with CYANA 2.1 on a workstation or U2 cluster

Jma at 17:41, 4 November 2009

2009-11-04T17:41:20Z

← Older revision		Revision as of 17:41, 4 November 2009
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	<br>		<br>

	-- ~~Main.~~AlexEletski - 10 Jul 2007		-- AlexEletski - 10 Jul 2007

			-- Edited by JimAramini - Nov 2009

Jma at 19:02, 3 November 2009

2009-11-03T19:02:59Z

← Older revision		Revision as of 19:02, 3 November 2009
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	= '''Manual structure calculation with CYANA 2.1''' =		= '''Manual structure calculation with CYANA 2.1''' =

	== '''Introduction''' ==		== '''Introduction''' ==

	Manual structure calculation is performed similar to the [[NoeassignCYANARun\|automated calculation]].		Manual structure calculation is performed similar to the [[NoeassignCYANARun\|automated calculation]].

Jma at 19:02, 3 November 2009

2009-11-03T19:02:14Z

← Older revision		Revision as of 19:02, 3 November 2009
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	== Manual structure calculation with CYANA 2.1 ==		= '''Manual structure calculation with CYANA 2.1''' =

			== '''Introduction''' ==

	Manual structure calculation is performed similar to the [[NoeassignCYANARun\|automated calculation]].		Manual structure calculation is performed similar to the [[NoeassignCYANARun\|automated calculation]].
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	<br>		<br>

	=== '''CALC.cya''' ===		== '''CALC.cya''' ==
	<pre>peaks  := n_cons,ali_cons,aro_cons # names of peak lists		<pre>peaks  := n_cons,ali_cons,aro_cons # names of peak lists
	prot  := $name # names of proton lists		prot  := $name # names of proton lists

Jma at 06:09, 1 November 2009

2009-11-01T06:09:28Z

Jma: moved NESG:ManualCYANARun to ManualCYANARun

2009-11-01T05:22:51Z

moved NESG:ManualCYANARun to ManualCYANARun

← Older revision	Revision as of 05:22, 1 November 2009
(No difference)

Jma at 05:18, 1 November 2009

2009-11-01T05:18:49Z

← Older revision		Revision as of 05:18, 1 November 2009
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	=== '''CALC.cya''' ===		=== '''CALC.cya''' ===
			<pre>peaks := n_cons,ali_cons,aro_cons # names of peak lists
	<~~nowiki~~>
	peaks := n_cons,ali_cons,aro_cons # names of peak lists
	prot := $name # names of proton lists		prot := $name # names of proton lists
	tolerance := 0.05,0.02,0.4 # chemical shift tolerances		tolerance := 0.05,0.02,0.4 # chemical shift tolerances
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	overview $name.ovw structures=20 pdb # write overview file and coordinates		overview $name.ovw structures=20 pdb # write overview file and coordinates
	#overview $name.ovw structures=20 significant=1 pdb		#overview $name.ovw structures=20 significant=1 pdb
	</~~nowiki~~>		</pre>


	Here <tt>expand=0</tt> is needed to correctly interpret UPLs created with CALIBA.		Here <tt>expand=0</tt> is needed to correctly interpret UPLs created with CALIBA.
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	Macro <tt>flip.cya</tt> can be used to flip the side chains Glu, Asp, Phe and Tyr to reduce RMSD in the final calculation.		Macro <tt>flip.cya</tt> can be used to flip the side chains Glu, Asp, Phe and Tyr to reduce RMSD in the final calculation.

	Overview by default will report only violation in at least <tt>structures/3</tt> conformers, and in this particular case these are six. To have all violations reported add <tt>significant=1</tt>.		Overview by default will report only violation in at least <tt>structures/3</tt> conformers, and in this particular case these are six. To have all violations reported add <tt>significant=1</tt>.

			Macro <tt>peakcheck</tt> verifies AtomList and peaklists for consistency and is very useful when manually assigned peaks are used.

	~~Macro <tt>peakcheck</tt> verifies AtomList and peaklists~~ for ~~consistency and is very useful when manually assigned peaks are used~~.		It is important to set peak volumes to their absolute values before calling caliba for calibration.

	~~It is important to set peak volumes to their absolute values before calling caliba for calibration.~~

	~~%COMMENT%~~

	-- Main.AlexEletski - 10 Jul 2007		-- Main.AlexEletski - 10 Jul 2007

← Older revision		Revision as of 06:09, 1 November 2009
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	== Manual structure calculation with CYANA 2.1 ==		== Manual structure calculation with CYANA 2.1 ==

	Manual structure calculation is performed similar to the [[~~NESG:~~NoeassignCYANARun\|automated calculation]].		Manual structure calculation is performed similar to the [[NoeassignCYANARun\|automated calculation]].

	# Create a new working subdirectory (<tt>structure/cyana21/calc3</tt>)		#Create a new working subdirectory (<tt>structure/cyana21/calc3</tt>)
	# Copy init.cya, XXXX.seq, XXXX.prot into this directiory.		#Copy init.cya, XXXX.seq, XXXX.prot into this directiory.
	# Export the latest peaklists, like n-cons, ali-cons and aro-cons.		#Export the latest peaklists, like n-cons, ali-cons and aro-cons.
	# Copy the latest <tt>stereofound.cya</tt> from the latest GridSearch run.		#Copy the latest <tt>stereofound.cya</tt> from the latest GridSearch run.
	# (Optional) Copy the <tt>talos.aco</tt> file		#(Optional) Copy the <tt>talos.aco</tt> file
	# Download the [[NESG:%ATTACHURL%/CALC.cya\|CALC.cya]] file (see below). Modify peaklist names, calibration parameters and tolerances.		#Download the [[NESG:%ATTACHURL%/CALC.cya\|CALC.cya]] file (see below). Modify peaklist names, calibration parameters and tolerances.
	# Run calculation with CYANA 2.1 on a workstation or U2 cluster		#Run calculation with CYANA 2.1 on a workstation or U2 cluster

			<br>

	=== '''CALC.cya''' ===		=== '''CALC.cya''' ===
	<pre>peaks := n_cons,ali_cons,aro_cons # names of peak lists		<pre>peaks  := n_cons,ali_cons,aro_cons # names of peak lists
	prot := $name # names of proton lists		prot  := $name # names of proton lists
	tolerance := 0.05,0.02,0.4 # chemical shift tolerances		tolerance  := 0.05,0.02,0.4 # chemical shift tolerances
	# order: 1H(a), 1H(b), 13C/15N(b), 13C/15N(a)		# order: 1H(a), 1H(b), 13C/15N(b), 13C/15N(a)
	if (master) then		if (master) then
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	overview $name.ovw structures=20 pdb # write overview file and coordinates		overview $name.ovw structures=20 pdb # write overview file and coordinates
	#overview $name.ovw structures=20 significant=1 pdb		#overview $name.ovw structures=20 significant=1 pdb
	</pre>		</pre>
			<br> Here <tt>expand=0</tt> is needed to correctly interpret UPLs created with CALIBA.

	Here <tt>expand=0</tt> is needed to correctly interpret UPLs created with CALIBA.

	Macro <tt>flip.cya</tt> can be used to flip the side chains Glu, Asp, Phe and Tyr to reduce RMSD in the final calculation.		Macro <tt>flip.cya</tt> can be used to flip the side chains Glu, Asp, Phe and Tyr to reduce RMSD in the final calculation.
Line 64:		Line 63:
	It is important to set peak volumes to their absolute values before calling caliba for calibration.		It is important to set peak volumes to their absolute values before calling caliba for calibration.

			<br>

	-- Main.AlexEletski - 10 Jul 2007		-- Main.AlexEletski - 10 Jul 2007