Overview of Consensus Runs - Revision history

Jma at 21:11, 6 January 2010

2010-01-06T21:11:33Z

← Older revision		Revision as of 21:11, 6 January 2010
Line 1:		Line 1:

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

Line 44:		Line 43:
	It is recommended to use [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Val and Leu methyl groups]] in automated structure calculation.		It is recommended to use [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Val and Leu methyl groups]] in automated structure calculation.

	Stereospecific assignments derived with [[FOUND\|FOUND]] should be applied with caution at this stage, because the may not be 100% correct.		Stereospecific assignments derived with [[FOUND\|FOUND]] should be applied with caution at this stage, because the may not be 100% correct.

	~~<br>~~

	~~-- David.Parish - 16 Apr 2007~~

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

Jma at 22:00, 5 November 2009

2009-11-05T22:00:27Z

← Older revision		Revision as of 22:00, 5 November 2009
Line 1:		Line 1:
	~~= '''Overview of Consensus Runs''' =~~

	== '''Introduction''' ==		== '''Introduction''' ==
Line 20:		Line 19:




	== '''External Constraints''' ==		== '''External Constraints''' ==
Line 28:		Line 27:
	There is some controversy about the use of initial short and intra UPLs constraints in automatic NOE assignment.<br> The ''pro'' arguments:		There is some controversy about the use of initial short and intra UPLs constraints in automatic NOE assignment.<br> The ''pro'' arguments:

	*Intra and short peak assignments are carefully checked.		*Intra and short peak assignments are carefully checked.
	*Intra and short-range constraints are verified with [[FOUND\|FOUND]] and [[ManualCYANARun\|manual CYANA run]].		*Intra and short-range constraints are verified with [[FOUND\|FOUND]] and [[ManualCYANARun\|manual CYANA run]].
	*Intra and short-range peak assignments are preserved during structure calculation, thus preventing incorrect assignments for these peaks.		*Intra and short-range peak assignments are preserved during structure calculation, thus preventing incorrect assignments for these peaks.
Line 39:		Line 38:
	*CYANA 2.1 uses "elastic" NOE calibration, relaxing consistently violated UPLs. Incorrect external constraints essentially block this feature.		*CYANA 2.1 uses "elastic" NOE calibration, relaxing consistently violated UPLs. Incorrect external constraints essentially block this feature.

	To resolve these issues it may be suggested to run two automatic structure calculations, one with intra and short external constraints, and one without. The numbers of derived UPLs and the numbers of assigned/unassigned peaks can then be compared.		To resolve these issues it may be suggested to run two automatic structure calculations, one with intra and short external constraints, and one without. The numbers of derived UPLs and the numbers of assigned/unassigned peaks can then be compared.

	== '''Stereospecific Assignments''' ==		== '''Stereospecific Assignments''' ==

Jma: moved OverviewOfConsensusRuns to Overview of Consensus Runs

2009-11-05T21:56:51Z

moved OverviewOfConsensusRuns to Overview of Consensus Runs

← Older revision	Revision as of 21:56, 5 November 2009
(No difference)

Jma at 02:42, 4 November 2009

2009-11-04T02:42:46Z

← Older revision		Revision as of 02:42, 4 November 2009
Line 1:		Line 1:
	= '''Overview of Consensus Runs''' =		= '''Overview of Consensus Runs''' =

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

	AutoStructure and CYANA 2.1 are used in parallel to run automatic structure calculations. Identical NOE assignments from both programs (''consensus assignments'') are accepted as the starting point for the next structure calculation. This protocol provides a conservative way to obtain reliable long range NOE assignments in an automatic manner. The main goal of consensus run is to obtain many reliable NOE assignments rather than to deliver a structure. Consensus assignments should deliver a structure with RMSD < 2 A, which makes subsequent manual refinement straightforward.<br>		AutoStructure and CYANA 2.1 are used in parallel to run automatic structure calculations. Identical NOE assignments from both programs (''consensus assignments'') are accepted as the starting point for the next structure calculation. This protocol provides a conservative way to obtain reliable long range NOE assignments in an automatic manner. The main goal of consensus run is to obtain many reliable NOE assignments rather than to deliver a structure. Consensus assignments should deliver a structure with RMSD < 2 A, which makes subsequent manual refinement straightforward.<br>

	[[Image:ConsensusMerge.jpg]]		[[Image:ConsensusMerge.jpg]]

	Input data:		Input data:
Line 16:		Line 16:
	*intra- and short-range UPLs and ACOs		*intra- and short-range UPLs and ACOs

	Prior to consensus verify chemical shift and peak assignments.		Prior to a consensus run verify chemical shift and peak assignments.

Jma at 02:39, 4 November 2009

2009-11-04T02:39:06Z

← Older revision		Revision as of 02:39, 4 November 2009
Line 39:		Line 39:
	To resolve these issues it may be suggested to run two automatic structure calculations, one with intra and short external constraints, and one without. The numbers of derived UPLs and the numbers of assigned/unassigned peaks can then be compared.		To resolve these issues it may be suggested to run two automatic structure calculations, one with intra and short external constraints, and one without. The numbers of derived UPLs and the numbers of assigned/unassigned peaks can then be compared.

	== '''Stereospecific ~~assignments~~''' ==		== '''Stereospecific Assignments''' ==

	It is recommended to use [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Val and Leu methyl groups]] in automated structure calculation.		It is recommended to use [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Val and Leu methyl groups]] in automated structure calculation.

Jma at 02:36, 4 November 2009

2009-11-04T02:36:40Z

← Older revision		Revision as of 02:36, 4 November 2009
Line 43:		Line 43:
	It is recommended to use [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Val and Leu methyl groups]] in automated structure calculation.		It is recommended to use [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Val and Leu methyl groups]] in automated structure calculation.

	[[FOUND\|~~Stereospecific assignments derived with~~ FOUND]] should be applied with caution at this stage, because the may not be 100% correct.		Stereospecific assignments derived with [[FOUND\|FOUND]] should be applied with caution at this stage, because the may not be 100% correct.


			<br>

	-- David.Parish - 16 Apr 2007		-- David.Parish - 16 Apr 2007

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

Jma at 02:34, 4 November 2009

2009-11-04T02:34:38Z

← Older revision		Revision as of 02:34, 4 November 2009
Line 20:		Line 20:


	== '''External Constraints''' ==		== '''External Constraints''' ==

	External constraints, such as TALOS dihedral angle constraints, are used to facilitate convergence to the correct structure.		External constraints, such as TALOS dihedral angle constraints, are used to facilitate convergence to the correct structure.

	There is some controversy about the use of initial short and intra UPLs constraints in automatic NOE assignment.<br/>		There is some controversy about the use of initial short and intra UPLs constraints in automatic NOE assignment.<br> The ''pro'' arguments:
	The ''pro'' arguments:
	* Intra and short peak assignments are carefully checked
	* Intra and short-range constraints are [[NESG:UsingFOUNDakaHABAS\|verified with FOUND and manual CYANA run]]
	* Intra and short-range peak assignments are preserved during structure calculation, thus preventing incorrect assignments for these peaks.
	* Improved convergence to the correct structure

	The ''contra'' arguments:		*Intra and short peak assignments are carefully checked.
	* Intra and short peaks frequently overlap with long-range peaks or the water line. Since the presence of long-range correlation is not known it may lead to overestimated peak integrals and too tight UPLs.		*Intra and short-range constraints are verified with [[FOUND\|FOUND]] and [[ManualCYANARun\|manual CYANA run]].
	* Some too tight UPLs may still be overlooked during [[~~NESG:UsingFOUNDakaHABAS~~\|~~verification with~~ FOUND and manual CYANA run]].		*Intra and short-range peak assignments are preserved during structure calculation, thus preventing incorrect assignments for these peaks.
	* CYANA 2.1 uses "elastic" NOE calibration, relaxing consistently violated UPLs. Incorrect external constraints essentially block this feature.		*Improved convergence to the correct structure.

			The ''contra'' arguments:

			*Intra and short peaks frequently overlap with long-range peaks or the water line. Since the presence of long-range correlation is not known it may lead to overestimated peak integrals and too tight UPLs.
			*Some too tight UPLs may still be overlooked during verification with [[FOUND\|FOUND]] and [[ManualCYANARun\|manual CYANA run]].
			*CYANA 2.1 uses "elastic" NOE calibration, relaxing consistently violated UPLs. Incorrect external constraints essentially block this feature.

	To resolve these issues it may be suggested to run two automatic structure calculations, one with intra and short external constraints, and one without. The numbers of derived UPLs and the numbers of assigned/unassigned peaks can then be compared.		To resolve these issues it may be suggested to run two automatic structure calculations, one with intra and short external constraints, and one without. The numbers of derived UPLs and the numbers of assigned/unassigned peaks can then be compared.


	== '''Stereospecific assignments''' ==		== '''Stereospecific assignments''' ==

Jma at 02:30, 4 November 2009

2009-11-04T02:30:51Z

← Older revision		Revision as of 02:30, 4 November 2009
Line 39:		Line 39:


	== '''Stereospecific assignments''' ==		== '''Stereospecific assignments''' ==

	It is recommended to use [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Val and Leu methyl groups]] in automated structure calculation.		It is recommended to use [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Val and Leu methyl groups]] in automated structure calculation.

	[[~~NESG:UsingFOUNDakaHABAS~~\|Stereospecific assignments derived with FOUND]] should be applied with caution at this stage, because the may not be 100% correct.		[[FOUND\|Stereospecific assignments derived with FOUND]] should be applied with caution at this stage, because the may not be 100% correct.

	~~%COMMENT%~~

	-- David.Parish - 16 Apr 2007
			-- David.Parish - 16 Apr 2007

			--Edited by JimAramini - Nov 2009

Jma at 02:27, 4 November 2009

2009-11-04T02:27:59Z

← Older revision		Revision as of 02:27, 4 November 2009
Line 1:		Line 1:
	== '''Overview of Consensus Runs''' ==		= '''Overview of Consensus Runs''' =

	~~AutoStructure and CYANA 2.1 are used in parallel to run automatic structure calculations. Identical NOE assignments from both programs (~~''~~consensus assignments~~'') are accepted as the starting point for the next structure calculation. This protocol provides a conservative way to obtain reliable long range NOE assignments in an automatic manner. The main goal of consensus run is to obtain many reliable NOE assignments rather than to deliver a structure. Consensus assignments should deliver a structure with RMSD < 2 A, which makes subsequent manual refinement straightforward.		== '''Introduction''' ==

	~~<img src="%ATTACHURLPATH%/merge~~.~~jpg" alt="merge~~.~~jpg" width=~~'~~617~~' ~~height=~~'~~462~~' />		AutoStructure and CYANA 2.1 are used in parallel to run automatic structure calculations. Identical NOE assignments from both programs (''consensus assignments'') are accepted as the starting point for the next structure calculation. This protocol provides a conservative way to obtain reliable long range NOE assignments in an automatic manner. The main goal of consensus run is to obtain many reliable NOE assignments rather than to deliver a structure. Consensus assignments should deliver a structure with RMSD < 2 A, which makes subsequent manual refinement straightforward.<br>

	~~Input data~~:		[[Image:ConsensusMerge.jpg]]
	* protein sequence
	* assigned chemical shifts
	* integrated NOESY peaklists
	* stereospecific assignments (recommended)
	* TALOS ACOs
	* intra- and short-range UPLs and ACOs

	Prior to consensus verify chemical shift and peak assignments.		Input data:

			*protein sequence
			*assigned chemical shifts
			*integrated NOESY peaklists
			*stereospecific assignments (recommended)
			*TALOS ACOs
			*intra- and short-range UPLs and ACOs

			Prior to consensus verify chemical shift and peak assignments.



	== '''External Constraints''' ==		== '''External Constraints''' ==

Jma: moved NESG:OverviewOfConsensusRuns to OverviewOfConsensusRuns

2009-11-04T02:16:48Z

moved NESG:OverviewOfConsensusRuns to OverviewOfConsensusRuns

← Older revision	Revision as of 02:16, 4 November 2009
(No difference)