GLOMSA - Revision history

Jma at 21:52, 6 January 2010

2010-01-06T21:52:27Z

← Older revision		Revision as of 21:52, 6 January 2010
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	<br>		<br>

	~~<br>~~

	~~-- Main.GaohuaLiu - 29 Jan 2007~~

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

	~~<br>~~

	*[[Media:Run_glomsa.cya\|run_glomsa.cya]]: CYANA script to run GLOMSA		*[[Media:Run_glomsa.cya\|run_glomsa.cya]]: CYANA script to run GLOMSA

Jma at 22:10, 5 November 2009

2009-11-05T22:10:07Z

← Older revision		Revision as of 22:10, 5 November 2009
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	*GLOMSA requires that you load a structure and UPL constraints. You should also declare the previously established stereospecific assignments (e.g., for VAL and LEU methyl groups) so that these could be used to determine new tereospecific assignments.<br>		*GLOMSA requires that you load a structure and UPL constraints. You should also declare the previously established stereospecific assignments (e.g., for VAL and LEU methyl groups) so that these could be used to determine new tereospecific assignments.<br>
	*'''Important!''' The UPL constraints supplied to GLOMSA must generated before distance modification with <tt>distance modify</tt>. When you follow the procedure in the [[ManualCYANARun\|manual structure calculation]] example this would be the <tt>$name-in.upl</tt> file.		*'''Important!''' The UPL constraints supplied to GLOMSA must generated before distance modification with <tt>distance modify</tt>. When you follow the procedure in the [[ManualCYANARun\|manual structure calculation]] example this would be the <tt>$name-in.upl</tt> file.
	*At this point we usually assign only HB2/3 spins and HA2/3 spins of Gly, HD21/22 of Asn and HE21/22 of Gln. Methyl QG1/2 of Val and QD1/2 of Leu can be assigned at this stage if that has not been done previously with the help of a fractionally ~~13C~~-labeled sample. Stereospecific assignments of other spin pair are usually not reliable.		*At this point we usually assign only HB2/3 spins and HA2/3 spins of Gly, HD21/22 of Asn and HE21/22 of Gln. Methyl QG1/2 of Val and QD1/2 of Leu can be assigned at this stage if that has not been done previously with the help of a fractionally <sup>13</sup>C-labeled sample. Stereospecific assignments of other spin pair are usually not reliable.
	*In the first iteration accept only stereospecific assignments supported by multiple third atoms.		*In the first iteration accept only stereospecific assignments supported by multiple third atoms.

Jma at 22:09, 5 November 2009

2009-11-05T22:09:33Z

← Older revision		Revision as of 22:09, 5 November 2009
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			== '''Introduction''' ==
	== '''~~Overview~~''' ==

	GLOMSA (GLObal Method for Stereospecific Assignment) is performed with the preliminary conformers and using all the local and global experimental data. If there are two NOEs of significantly different strength from a given proton to both diastereotopic substituents of a prochiral center and if the distances from the given proton to the two diastereotopic substituents differ consistently in the structures, the stronger NOE can be identified with the diastereotopic substituent that is closer to the given proton.		GLOMSA (GLObal Method for Stereospecific Assignment) is performed with the preliminary conformers and using all the local and global experimental data. If there are two NOEs of significantly different strength from a given proton to both diastereotopic substituents of a prochiral center and if the distances from the given proton to the two diastereotopic substituents differ consistently in the structures, the stronger NOE can be identified with the diastereotopic substituent that is closer to the given proton.

Jma at 22:09, 5 November 2009

2009-11-05T22:09:09Z

← Older revision		Revision as of 22:09, 5 November 2009
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	~~= '''SSA with GLOMSA (GLObal Method for Stereospecific Assignment) Module''' =~~

	== '''Overview''' ==		== '''Overview''' ==

	GLOMSA is performed with the preliminary conformers and using all the local and global experimental data. If there are two NOEs of significantly different strength from a given proton to both diastereotopic substituents of a prochiral center and if the distances from the given proton to the two diastereotopic substituents differ consistently in the structures, the stronger NOE can be identified with the diastereotopic substituent that is closer to the given proton.		GLOMSA (GLObal Method for Stereospecific Assignment) is performed with the preliminary conformers and using all the local and global experimental data. If there are two NOEs of significantly different strength from a given proton to both diastereotopic substituents of a prochiral center and if the distances from the given proton to the two diastereotopic substituents differ consistently in the structures, the stronger NOE can be identified with the diastereotopic substituent that is closer to the given proton.

	[[Image:Glomsa1.jpg]]		[[Image:Glomsa1.jpg]]
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	4.  Big violations should be detected if the opposite stereospecific assignment is used.		4.  Big violations should be detected if the opposite stereospecific assignment is used.

	<br>		<br>

	=== '''run_glomsa.cya''' ===		=== '''run_glomsa.cya''' ===
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	-- Main.GaohuaLiu - 29 Jan 2007		-- Main.GaohuaLiu - 29 Jan 2007

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

	<br>		<br>

	*[[Media:Run_glomsa.cya\|run_glomsa.cya]]: CYANA script to run GLOMSA		*[[Media:Run_glomsa.cya\|run_glomsa.cya]]: CYANA script to run GLOMSA

Jma at 17:26, 4 November 2009

2009-11-04T17:26:59Z

← Older revision		Revision as of 17:26, 4 November 2009
Line 92:		Line 92:

	-- Main.GaohuaLiu - 29 Jan 2007		-- Main.GaohuaLiu - 29 Jan 2007

			-- Edited by JimAramini - Nov 2009

	<br>		<br>

	*[[Media:Run_glomsa.cya\|run_glomsa.cya]]: CYANA script to run GLOMSA		*[[Media:Run_glomsa.cya\|run_glomsa.cya]]: CYANA script to run GLOMSA

Jma at 17:26, 4 November 2009

2009-11-04T17:26:32Z

← Older revision		Revision as of 17:26, 4 November 2009
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	2.  Verify that the NOE peak intensities (a-b1 and a-b2) are correct, and not biased by overlap with other peaks.		2.  Verify that the NOE peak intensities (a-b1 and a-b2) are correct, and not biased by overlap with other peaks.

	3.  Verify that the NOE peak intensities have not been misinterpreted (Example: HN-HB2 peak only resolved in <tt>n.peaks</tt>, and HN-HB3 - only in ali.peaks. Different NOE calibration ~~       ~~ constants for both peaklists may lead to incorrect stereospecific assignments).		3.  Verify that the NOE peak intensities have not been misinterpreted (Example: HN-HB2 peak only resolved in <tt>n.peaks</tt>, and HN-HB3 - only in ali.peaks. Different NOE calibration constants for both peaklists may lead to incorrect stereospecific assignments).

	4.  Big violations should be detected if the opposite stereospecific assignment is used.		4.  Big violations should be detected if the opposite stereospecific assignment is used.

	<br>		<br>

	=== '''run_glomsa.cya''' ===		=== '''run_glomsa.cya''' ===

Jma at 17:26, 4 November 2009

2009-11-04T17:26:01Z

← Older revision		Revision as of 17:26, 4 November 2009
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	#Copy the latest manual refinement directory.		#Copy the latest manual refinement directory.
	#Download the sample [[~~media~~:~~run glomsa~~.cya\|run_glomsa.cya]] script		#Download the sample [[Media:Run_glomsa.cya\|run_glomsa.cya]] script
	#Start CYANA 2.1 on a workstation and execute <tt>run_glomsa.cya</tt>. This will generate <tt>glomsa.out</tt> file.		#Start CYANA 2.1 on a workstation and execute <tt>run_glomsa.cya</tt>. This will generate <tt>glomsa.out</tt> file.
	#Analyze the output (here <tt>glomsa.out</tt>). For each stereospecific assignments verify that it is justified. Add confirmed assignments to the <tt>stereofound.cya</tt> file.		#Analyze the output (here <tt>glomsa.out</tt>). For each stereospecific assignments verify that it is justified. Add confirmed assignments to the <tt>stereofound.cya</tt> file.
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	*GLOMSA requires that you load a structure and UPL constraints. You should also declare the previously established stereospecific assignments (e.g., for VAL and LEU methyl groups) so that these could be used to determine new tereospecific assignments.<br>		*GLOMSA requires that you load a structure and UPL constraints. You should also declare the previously established stereospecific assignments (e.g., for VAL and LEU methyl groups) so that these could be used to determine new tereospecific assignments.<br>
	*'''Important!''' The UPL constraints supplied to GLOMSA must generated before distance modification with <tt>distance modify</tt>. When you follow the procedure in the [[~~NESG:~~ManualCYANARun\|manual structure calculation]] example this would be the <tt>$name-in.upl</tt> file.		*'''Important!''' The UPL constraints supplied to GLOMSA must generated before distance modification with <tt>distance modify</tt>. When you follow the procedure in the [[ManualCYANARun\|manual structure calculation]] example this would be the <tt>$name-in.upl</tt> file.
	*At this point we usually assign only HB2/3 spins and HA2/3 spins of Gly, HD21/22 of Asn and HE21/22 of Gln. Methyl QG1/2 of Val and QD1/2 of Leu can be assigned at this stage if that has not been done previously with the help of a fractionally 13C-labeled sample. Stereospecific assignments of other spin pair are usually not reliable.		*At this point we usually assign only HB2/3 spins and HA2/3 spins of Gly, HD21/22 of Asn and HE21/22 of Gln. Methyl QG1/2 of Val and QD1/2 of Leu can be assigned at this stage if that has not been done previously with the help of a fractionally 13C-labeled sample. Stereospecific assignments of other spin pair are usually not reliable.
	*In the first iteration accept only stereospecific assignments supported by multiple third atoms.		*In the first iteration accept only stereospecific assignments supported by multiple third atoms.
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	<br>		<br>

	*[[~~media~~:~~run glomsa~~.cya\|run_glomsa.cya]]: CYANA script to run GLOMSA		*[[Media:Run_glomsa.cya\|run_glomsa.cya]]: CYANA script to run GLOMSA

Jma at 17:23, 4 November 2009

2009-11-04T17:23:25Z

← Older revision		Revision as of 17:23, 4 November 2009
Line 95:		Line 95:
	<br>		<br>

	*[[~~NESG~~:~~%ATTACHURL%/~~run glomsa.cya\|run_glomsa.cya]]: CYANA script to run GLOMSA		*[[media:run glomsa.cya\|run_glomsa.cya]]: CYANA script to run GLOMSA

Jma at 17:22, 4 November 2009

2009-11-04T17:22:45Z

← Older revision		Revision as of 17:22, 4 November 2009
Line 23:		Line 23:

	#Copy the latest manual refinement directory.		#Copy the latest manual refinement directory.
	#Download the sample [[~~NESG~~:~~%ATTACHURL%/~~run glomsa.cya\|run_glomsa.cya]] script		#Download the sample [[media:run glomsa.cya\|run_glomsa.cya]] script
	#Start CYANA 2.1 on a workstation and execute <tt>run_glomsa.cya</tt>. This will generate <tt>glomsa.out</tt> file.		#Start CYANA 2.1 on a workstation and execute <tt>run_glomsa.cya</tt>. This will generate <tt>glomsa.out</tt> file.
	#Analyze the output (here <tt>glomsa.out</tt>). For each stereospecific assignments verify that it is justified. Add confirmed assignments to the <tt>stereofound.cya</tt> file.		#Analyze the output (here <tt>glomsa.out</tt>). For each stereospecific assignments verify that it is justified. Add confirmed assignments to the <tt>stereofound.cya</tt> file.
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	Exceptions:		Exceptions:

	*Some conflicting results may be caused by NOE peaks to QD and QE pseudoatoms of aromatic rings, due to constituent HD1/2 and HE1/2 atoms being so far away from the pseudoatom and slow ring flipping.		*Some conflicting results may be caused by NOE peaks to QD and QE pseudoatoms of aromatic rings, due to constituent HD1/2 and HE1/2 atoms being so far away from the pseudoatom and slow ring flipping.
	*Some conflicting results may be caused by incorrect peak intensities (see next point).		*Some conflicting results may be caused by incorrect peak intensities (see next point).

	2.  Verify that the NOE peak intensities (a-b1 and a-b2) are correct, and not biased by overlap with other peaks.		2.  Verify that the NOE peak intensities (a-b1 and a-b2) are correct, and not biased by overlap with other peaks.

	3.  Verify that the NOE peak intensities have not been misinterpreted (Example: HN-HB2 peak only resolved in <tt>n.peaks</tt>, and HN-HB3 - only in ali.peaks. Different NOE calibration         constants for both peaklists may lead to incorrect stereospecific assignments).		3.  Verify that the NOE peak intensities have not been misinterpreted (Example: HN-HB2 peak only resolved in <tt>n.peaks</tt>, and HN-HB3 - only in ali.peaks. Different NOE calibration         constants for both peaklists may lead to incorrect stereospecific assignments).

	4.  Big violations should be detected if the opposite stereospecific assignment is used.		4.  Big violations should be detected if the opposite stereospecific assignment is used.

	<br>		<br>

	=== '''run_glomsa.cya''' ===		=== '''run_glomsa.cya''' ===

Jma at 18:49, 3 November 2009

2009-11-03T18:49:43Z

← Older revision		Revision as of 18:49, 3 November 2009
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	=== '''Acceptance criteria for stereospecific assignments from GLOMSA''' ===		=== '''Acceptance criteria for stereospecific assignments from GLOMSA''' ===

	1. No conflicting stereospecific assignments in the output of GLOMSA (for example, both <tt>as input</tt> and <tt>reversed</tt> assignments for the same atom pair).		1.  No conflicting stereospecific assignments in the output of GLOMSA (for example, both <tt>as input</tt> and <tt>reversed</tt> assignments for the same atom pair).

	Exceptions:		Exceptions:
	**Some conflicting results may be caused by NOE peaks to QD and QE pseudoatoms of aromatic rings, due to constituent HD1/2 and HE1/2 atoms being so far away from the pseudoatom and slow ring flipping.
	**Some conflicting results may be caused by incorrect peak intensities (see next point).		*Some conflicting results may be caused by NOE peaks to QD and QE pseudoatoms of aromatic rings, due to constituent HD1/2 and HE1/2 atoms being so far away from the pseudoatom and slow ring flipping.
	2. Verify that the NOE peak intensities (a-b1 and a-b2) are correct, and not biased by overlap with other peaks.		*Some conflicting results may be caused by incorrect peak intensities (see next point).
	3. Verify that the NOE peak intensities have not been misinterpreted (Example: HN-HB2 peak only resolved in <tt>n.peaks</tt>, and HN-HB3 - only in ali.peaks. Different NOE calibration constants for both peaklists may lead to incorrect stereospecific assignments.)
	4. Big violations should be detected if the opposite stereospecific assignment is used.		2.  Verify that the NOE peak intensities (a-b1 and a-b2) are correct, and not biased by overlap with other peaks.

			3.  Verify that the NOE peak intensities have not been misinterpreted (Example: HN-HB2 peak only resolved in <tt>n.peaks</tt>, and HN-HB3 - only in ali.peaks. Different NOE calibration         constants for both peaklists may lead to incorrect stereospecific assignments).

			4.  Big violations should be detected if the opposite stereospecific assignment is used.

	<br>		<br>