AVS - Revision history

Jma at 16:56, 5 January 2010

2010-01-05T16:56:20Z

← Older revision		Revision as of 16:56, 5 January 2010
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	Assignment validation suite ([http://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC residue/atom naming, chemical shifts that are widely outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. percents assignments, number of stereospecifically assigned methyls, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and is included as part of the Protein Structure Validation Suite (PSVS).		Assignment validation suite ([http://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC residue/atom naming, chemical shifts that are widely outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. percents assignments, number of stereospecifically assigned methyls, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and is included as part of the Protein Structure Validation Suite (PSVS).

	<br>		<br>

	== '''Practical Aspects''' ==		== '''Practical Aspects''' ==

	=== Running AVS ===		=== Running AVS ===

	A number of version for the standalone AVS routine exist that are adapted for different bmrb versions  (2.1 or 3.1). Two perl scripts can be run from any directory on any computer running perl by either pointing to the local AutoAssign script repository directory or by downloading the scripts linked below.  Here an example script is provideded that generates the bmrb in 2.1 format directly from the sparky resonance list 'rl' and the protein sequences.  The script validates and computes the completeness statistics for the generated chemical shift list.  As modifications are made in the sparky project the operation is repeated until a final bmrb file is achieved.<br>		A number of version for the standalone AVS routine exist that are adapted for different bmrb versions  (2.1 or 3.1). Two perl scripts can be run from any directory on any computer running perl by either pointing to the local AutoAssign script repository directory or by downloading the scripts linked below.  Here an example script is provideded that generates the bmrb in 2.1 format directly from the sparky resonance list 'rl' and the protein sequences.  The script validates and computes the completeness statistics for the generated chemical shift list.  As modifications are made in the sparky project the operation is repeated until a final bmrb file is achieved.<br>
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	</pre>		</pre>
	<br>		<br>

	~~<br>~~

	~~-- PaoloRossi - 20 Nov 2009~~

AlexLemak at 21:23, 18 December 2009

2009-12-18T21:23:38Z

← Older revision		Revision as of 21:23, 18 December 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	Assignment validation suite ([http://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC residue/atom naming, chemical shifts that are widely outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. ~~percent~~ assignments, number of stereospecifically assigned ~~methlys~~, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and is included as part of the Protein Structure Validation Suite (PSVS).		Assignment validation suite ([http://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC residue/atom naming, chemical shifts that are widely outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. percents assignments, number of stereospecifically assigned methyls, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and is included as part of the Protein Structure Validation Suite (PSVS).

	<br>		<br>

	== '''Practical Aspects''' ==		== '''Practical Aspects''' ==

Prossi at 20:39, 14 December 2009

2009-12-14T20:39:25Z

← Older revision		Revision as of 20:39, 14 December 2009
Line 56:		Line 56:
	<br>		<br>

	Below is a view of the missing_shift.pl script.  For the protein in the example backbone assignment only was conducted (unlisted atoms are present in the bmrb):		Below is a view of the missing_shift.pl script.  For the protein in the example, backbone assignment only was conducted (unlisted atoms are present in the bmrb):
	<pre>D189: HB2 HB3		<pre>D189: HB2 HB3
	L190: CD1 CD2 CG HB2 HB3 HD1 HD2 HG		L190: CD1 CD2 CG HB2 HB3 HD1 HD2 HG

Jma at 21:47, 23 November 2009

2009-11-23T21:47:12Z

← Older revision		Revision as of 21:47, 23 November 2009
Line 6:		Line 6:

	== '''Practical Aspects''' ==		== '''Practical Aspects''' ==

			=== Running AVS ===

	A number of version for the standalone AVS routine exist that are adapted for different bmrb versions  (2.1 or 3.1). Two perl scripts can be run from any directory on any computer running perl by either pointing to the local AutoAssign script repository directory or by downloading the scripts linked below.  Here an example script is provideded that generates the bmrb in 2.1 format directly from the sparky resonance list 'rl' and the protein sequences.  The script validates and computes the completeness statistics for the generated chemical shift list.  As modifications are made in the sparky project the operation is repeated until a final bmrb file is achieved.<br>		A number of version for the standalone AVS routine exist that are adapted for different bmrb versions  (2.1 or 3.1). Two perl scripts can be run from any directory on any computer running perl by either pointing to the local AutoAssign script repository directory or by downloading the scripts linked below.  Here an example script is provideded that generates the bmrb in 2.1 format directly from the sparky resonance list 'rl' and the protein sequences.  The script validates and computes the completeness statistics for the generated chemical shift list.  As modifications are made in the sparky project the operation is repeated until a final bmrb file is achieved.<br>
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	<br>		<br>

	== '''Output interpretation''' ==		=== '''Output interpretation''' ===

	The output interpretation is straightforward. A view of the output for res. 189-191 from the validation script is shown below, the summary of errors at the bottom of the file provides quick list of overall problems to the scientist:<br>		The output interpretation is straightforward. A view of the output for res. 189-191 from the validation script is shown below, the summary of errors at the bottom of the file provides quick list of overall problems to the scientist:<br>

Jma at 21:46, 23 November 2009

2009-11-23T21:46:25Z

← Older revision		Revision as of 21:46, 23 November 2009
Line 1:		Line 1:
	= '''Introduction''' =		== '''Introduction''' ==

	Assignment validation suite ([http://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC residue/atom naming, chemical shifts that are widely outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. percent assignments, number of stereospecifically assigned methlys, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and is included as part of the Protein Structure Validation Suite (PSVS).		Assignment validation suite ([http://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC residue/atom naming, chemical shifts that are widely outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. percent assignments, number of stereospecifically assigned methlys, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and is included as part of the Protein Structure Validation Suite (PSVS).

			<br>

			== '''Practical Aspects''' ==
	=== Practical Aspects ===

	A number of version for the standalone AVS routine exist that are adapted for different bmrb versions  (2.1 or 3.1). Two perl scripts can be run from any directory on any computer running perl by either pointing to the local AutoAssign script repository directory or by downloading the scripts linked below.  Here an example script is provideded that generates the bmrb in 2.1 format directly from the sparky resonance list 'rl' and the protein sequences.  The script validates and computes the completeness statistics for the generated chemical shift list.  As modifications are made in the sparky project the operation is repeated until a final bmrb file is achieved.<br>		A number of version for the standalone AVS routine exist that are adapted for different bmrb versions  (2.1 or 3.1). Two perl scripts can be run from any directory on any computer running perl by either pointing to the local AutoAssign script repository directory or by downloading the scripts linked below.  Here an example script is provideded that generates the bmrb in 2.1 format directly from the sparky resonance list 'rl' and the protein sequences.  The script validates and computes the completeness statistics for the generated chemical shift list.  As modifications are made in the sparky project the operation is repeated until a final bmrb file is achieved.<br>
Line 21:		Line 21:
	<br>		<br>

	=== Output interpretation ===		== '''Output interpretation''' ==

	The output interpretation is straightforward. A view of the output for res. 189-191 from the validation script is shown below, the summary of errors at the bottom of the file provides quick list of overall problems to the scientist:<br>		The output interpretation is straightforward. A view of the output for res. 189-191 from the validation script is shown below, the summary of errors at the bottom of the file provides quick list of overall problems to the scientist:<br>

Prossi at 21:38, 23 November 2009

2009-11-23T21:38:05Z

← Older revision		Revision as of 21:38, 23 November 2009
Line 1:		Line 1:
	= '''Introduction''' =		= '''Introduction''' =

	Assignment validation suite ([http://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC residue/atom naming, chemical shifts that are widely outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. percent assignments, number of stereospecifically assigned methlys, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and is included as part of the Protein Structure Validation Suite (PSVS).  It is wise to run any chemical shift validation prior to structure determination, and uncover problems with the assignments that could impact the performance of noesy assignments and structure calculation downstream.		Assignment validation suite ([http://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC residue/atom naming, chemical shifts that are widely outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. percent assignments, number of stereospecifically assigned methlys, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and is included as part of the Protein Structure Validation Suite (PSVS).


	~~<br>~~

	=== Practical Aspects ===		=== Practical Aspects ===
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	</pre>		</pre>
	Several issues are flagged in the error summary for this entry, proton frequency out of range and CB for R132 out of range to indicate possible mis-assignment.		Several issues are flagged in the error summary for this entry, proton frequency out of range and CB for R132 out of range to indicate possible mis-assignment.


			<br>

	Below is a view of the missing_shift.pl script.  For the protein in the example backbone assignment only was conducted (unlisted atoms are present in the bmrb):		Below is a view of the missing_shift.pl script.  For the protein in the example backbone assignment only was conducted (unlisted atoms are present in the bmrb):

Prossi at 21:32, 23 November 2009

2009-11-23T21:32:41Z

← Older revision		Revision as of 21:32, 23 November 2009
Line 24:		Line 24:

	The output interpretation is straightforward. A view of the output for res. 189-191 from the validation script is shown below, the summary of errors at the bottom of the file provides quick list of overall problems to the scientist:<br>		The output interpretation is straightforward. A view of the output for res. 189-191 from the validation script is shown below, the summary of errors at the bottom of the file provides quick list of overall problems to the scientist:<br>
	<pre>		<pre>D189 Overall: Consistent Typing: Consistent SRO: Consistent C Shifts: Consistent H Shifts: Consistent
	D189 Overall: Consistent Typing: Consistent SRO: Consistent C Shifts: Consistent H Shifts: Consistent
	PRTL>> D 0.28 L 0.17 N 0.12 C 0.11 K 0.09 F 0.09 Y 0.08 R 0.01		PRTL>> D 0.28 L 0.17 N 0.12 C 0.11 K 0.09 F 0.09 Y 0.08 R 0.01
	HN Overlap>> D13 R126		HN Overlap>> D13 R126
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	</pre>		</pre>
	~~Here~~ is a view of the missing_shift.pl script.  For the protein in the example backbone assignment only was conducted:		Several issues are flagged in the error summary for this entry, proton frequency out of range and CB for R132 out of range to indicate possible mis-assignment.



			Below is a view of the missing_shift.pl script.  For the protein in the example backbone assignment only was conducted (unlisted atoms are present in the bmrb):
	<pre>D189: HB2 HB3		<pre>D189: HB2 HB3
	L190: CD1 CD2 CG HB2 HB3 HD1 HD2 HG		L190: CD1 CD2 CG HB2 HB3 HD1 HD2 HG

Prossi at 21:26, 23 November 2009

2009-11-23T21:26:41Z

← Older revision		Revision as of 21:26, 23 November 2009
Line 1:		Line 1:
	= '''Introduction''' =		= '''Introduction''' =

	Assignment validation suite ([http://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC~~ labeling~~, chemical shifts that are ~~grossly~~ outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. percent assignments, number of stereospecifically assigned methlys, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and ~~can be~~ included as part of the Protein Structure Validation Suite (PSVS) ~~run~~.  It is ~~advisable~~ to run any chemical shift validation prior to structure determination ~~steps in order to~~ uncover problems with the assignments that could impact the performance of noesy assignments and structure calculation downstream.		Assignment validation suite ([http://www.ncbi.nlm.nih.gov/pubmed/14872126 AVS]) checks the chemical shifts list in BioMagResBank (BMRB) format for a number of possible problems such as consistency to IUPAC residue/atom naming, chemical shifts that are widely outside the typical range for the particular atom/residue, and reports useful statistics information about the examined chemical shift set (e.g. percent assignments, number of stereospecifically assigned methlys, percents aromatic sidechain assignments, etc).   AVS is run on every chemical shift set that is submitted to the BMRB, and is included as part of the Protein Structure Validation Suite (PSVS).  It is wise to run any chemical shift validation prior to structure determination, and uncover problems with the assignments that could impact the performance of noesy assignments and structure calculation downstream.

	<br>		<br>
Line 19:		Line 19:
	Newer file versions are available in later versions of the AutoAssign program that should handle bmrb 3.1 format.		Newer file versions are available in later versions of the AutoAssign program that should handle bmrb 3.1 format.

			<br>

			=== Output interpretation ===
	=== Output interpretation ===

	The output interpretation is straightforward. A view of the output for res. 189-191 from the validation script is shown below, the summary of errors at the bottom of the file provides quick list of overall problems to the scientist:<br>		The output interpretation is straightforward. A view of the output for res. 189-191 from the validation script is shown below, the summary of errors at the bottom of the file provides quick list of overall problems to the scientist:<br>
	<pre>		<pre>

	D189 Overall: Consistent Typing: Consistent SRO: Consistent C Shifts: Consistent H Shifts: Consistent		D189 Overall: Consistent Typing: Consistent SRO: Consistent C Shifts: Consistent H Shifts: Consistent
	PRTL>> D 0.28 L 0.17 N 0.12 C 0.11 K 0.09 F 0.09 Y 0.08 R 0.01		PRTL>> D 0.28 L 0.17 N 0.12 C 0.11 K 0.09 F 0.09 Y 0.08 R 0.01
	HN Overlap>> D13 R126		HN Overlap>> D13 R126
	C Shift Assignments>> C :: 176.670 CA :: 54.404 CB :: 40.809		C Shift Assignments>> C :: 176.670 CA :: 54.404 CB :: 40.809
	H Shift Assignments>> H :: 8.458 HA :: 4.591		H Shift Assignments>> H :: 8.458 HA :: 4.591

	L190 Overall: Consistent Typing: Consistent SRO: Consistent C Shifts: Consistent H Shifts: Consistent		L190 Overall: Consistent Typing: Consistent SRO: Consistent C Shifts: Consistent H Shifts: Consistent
	PRTL>> L 0.22 K 0.2 D 0.14 R 0.12 C 0.1 F 0.09 Y 0.07 N 0.02		PRTL>> L 0.22 K 0.2 D 0.14 R 0.12 C 0.1 F 0.09 Y 0.07 N 0.02
	HN Overlap>> A20		HN Overlap>> A20
	C Shift Assignments>> C :: 177.898 CA :: 55.723 CB :: 41.968		C Shift Assignments>> C :: 177.898 CA :: 55.723 CB :: 41.968
	H Shift Assignments>> H :: 8.115 HA :: 4.191		H Shift Assignments>> H :: 8.115 HA :: 4.191

	E191 Overall: Consistent Typing: Consistent SRO: Consistent C Shifts: Consistent H Shifts: Consistent		E191 Overall: Consistent Typing: Consistent SRO: Consistent C Shifts: Consistent H Shifts: Consistent
	PRTL>> E 0.14 H 0.13 W 0.13 R 0.13 Q 0.13 C 0.11 K 0.1 M 0.05 I 0.02 V 0.01		PRTL>> E 0.14 H 0.13 W 0.13 R 0.13 Q 0.13 C 0.11 K 0.1 M 0.05 I 0.02 V 0.01
	C Shift Assignments>> C :: 176.524 CA :: 57.003 CB :: 29.910		C Shift Assignments>> C :: 176.524 CA :: 57.003 CB :: 29.910
	H Shift Assignments>> H :: 8.226 HA :: 4.107		H Shift Assignments>> H :: 8.226 HA :: 4.107

	Error Summary:		Error Summary:
Line 51:		Line 50:
	T181 HA = 2.217(S), Expected = 4.48, Std = 0.5000, ChiSquare = 6.0111e-06		T181 HA = 2.217(S), Expected = 4.48, Std = 0.5000, ChiSquare = 6.0111e-06

	</pre>		</pre>
	Here is a view of the missing_shift.pl script~~, for~~ the protein in the example backbone assignment only was conducted:		Here is a view of the missing_shift.pl script.  For the protein in the example backbone assignment only was conducted:
	<pre>D189: HB2 HB3		<pre>D189: HB2 HB3
	L190: CD1 CD2 CG HB2 HB3 HD1 HD2 HG		L190: CD1 CD2 CG HB2 HB3 HD1 HD2 HG
Line 58:		Line 57:

	AtomType Completeness Statistics:		AtomType Completeness Statistics:
	aromatic completeness :: 0 / 174 = 0.00%		aromatic completeness :: 0 / 174 = 0.00%
	backbone completeness :: 845 / 965 = 87.56%		backbone completeness :: 845 / 965 = 87.56%
	sidechain completeness :: 227 / 1244 = 18.25%		sidechain completeness :: 227 / 1244 = 18.25%
	unambiguous CH2 completeness :: 0 / 20 = 0.00%		unambiguous CH2 completeness :: 0 / 20 = 0.00%
	unambiguous CH3 completeness :: 0 / 32 = 0.00%		unambiguous CH3 completeness :: 0 / 32 = 0.00%


	C :: 168 / 197 = 85.28%		C :: 168 / 197 = 85.28%
	CA :: 181 / 197 = 91.88%		CA :: 181 / 197 = 91.88%
	CB :: 167 / 183 = 91.26%		CB :: 167 / 183 = 91.26%
	H :: 160 / 180 = 88.89%		H :: 160 / 180 = 88.89%
	HA :: 156 / 183 = 85.25%		HA :: 156 / 183 = 85.25%
	HA2 :: 11 / 14 = 78.57%		HA2 :: 11 / 14 = 78.57%
	HA3 :: 9 / 14 = 64.29%		HA3 :: 9 / 14 = 64.29%
	HB :: 8 / 56 = 14.29%		HB :: 8 / 56 = 14.29%

	</pre>		</pre>
			<br>



	~~Editing in progress~~

	<br>		<br>

	~~PaoLo roSSi~~		-- PaoloRossi - 20 Nov 2009

Prossi at 21:21, 23 November 2009

2009-11-23T21:21:29Z

@@ Line 15: / Line 15: @@
 cp test_bmrb.bmrb HsR50_bb.bmrb
 rm test_bmrb.bmrb</pre>
-<br> Three scripts are run: 1) [[Media:SparkyRL2bmrb.txt|sparkyRL2bmrb.pl]], 2) [[Media:Missing_shifts.txt|missing_shifts.pl]], and 3) [[Media:Validate_assignments.txt|validate_assignments.pl]]. In addition, a bmrb parsing module [[Media:BMRBParsing.pm|BMRBParsing.pm]] is called that interprets the sequence in single letter code and numbers the bmrb residues, ind this case starting from 1.
+<br> Three scripts are run: 1) [[Media:SparkyRL2bmrb.txt|sparkyRL2bmrb.pl]], 2) [[Media:Missing_shifts.txt|missing_shifts.pl]], and 3) [[Media:Validate_assignments.txt|validate_assignments.pl]]. In addition, a bmrb parsing module [[Media:BMRBParsing.pm|BMRBParsing.pm]] is called that interprets the sequence in single letter code and returns numbering in the bmrb file, in this case starting from residue 1.
 Newer file versions are available in later versions of the AutoAssign program that should handle bmrb 3.1 format.
 <br>
 Editing in progress

Prossi at 21:02, 23 November 2009

2009-11-23T21:02:57Z

← Older revision		Revision as of 21:02, 23 November 2009
Line 15:		Line 15:
	cp test_bmrb.bmrb HsR50_bb.bmrb		cp test_bmrb.bmrb HsR50_bb.bmrb
	rm test_bmrb.bmrb</pre>		rm test_bmrb.bmrb</pre>
	<br> Three scripts are run: 1) [[Media:SparkyRL2bmrb.txt\|sparkyRL2bmrb.pl]], 2) [[Media:Missing_shifts.txt\|missing_shifts.pl]], and 3) [[Media:~~validate_assignments~~.txt\|validate_assignments.pl]]. In addition, a bmrb parsing module [[Media:~~BMRBparsing~~.pm\|~~BMRBparsing~~.pm]] is called that interprets the sequence in single letter code and numbers the bmrb residues, ind this case starting from 1.		<br> Three scripts are run: 1) [[Media:SparkyRL2bmrb.txt\|sparkyRL2bmrb.pl]], 2) [[Media:Missing_shifts.txt\|missing_shifts.pl]], and 3) [[Media:Validate_assignments.txt\|validate_assignments.pl]]. In addition, a bmrb parsing module [[Media:BMRBParsing.pm\|BMRBParsing.pm]] is called that interprets the sequence in single letter code and numbers the bmrb residues, ind this case starting from 1.

	Newer file versions are available in later versions of the AutoAssign program that should handle bmrb 3.1 format.		Newer file versions are available in later versions of the AutoAssign program that should handle bmrb 3.1 format.