Validation of Consensus Run - Revision history

Jma at 21:15, 6 January 2010

2010-01-06T21:15:28Z

← Older revision		Revision as of 21:15, 6 January 2010
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	#The yield of consensus assigned NOEs shall be large than 50%.		#The yield of consensus assigned NOEs shall be large than 50%.

	<br>		<br>

	== '''Example scripts''' ==		== '''Example scripts''' ==
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	write upl cons.upl		write upl cons.upl
	protocol:=</pre>		protocol:=</pre>
	<br> <br> ~~-- GaohuaLiu - 26 Jan 2007~~		<br> <br><br>

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

Jma at 22:03, 5 November 2009

2009-11-05T22:03:06Z

← Older revision		Revision as of 22:03, 5 November 2009
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			== '''Verification of Consensus Assignments''' ==
	=== '''Verification of Consensus Assignments''' ===

	1.  Create a working subdirectory, for example, <tt>cyana21/calc2</tt>.		1.  Create a working subdirectory, for example, <tt>cyana21/calc2</tt>.
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	You may want to run an additional iteration of consensus assignment, though it is usually not necessary.<br>		You may want to run an additional iteration of consensus assignment, though it is usually not necessary.<br>

	=== '''Acceptance Criteria''' ===		== '''Acceptance Criteria''' ==

	A successful consensus run shall satisfy:		A successful consensus run shall satisfy:
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	#The yield of consensus assigned NOEs shall be large than 50%.		#The yield of consensus assigned NOEs shall be large than 50%.

	~~===~~		<br>

	=== '''Example scripts''' ===		== '''Example scripts''' ==

	==== '''run_caliba.cya''' ====		=== '''run_caliba.cya''' ===
	<pre>protocol:=caliba.log		<pre>protocol:=caliba.log
	read prot $name		read prot $name

Jma at 22:01, 5 November 2009

2009-11-05T22:01:48Z

← Older revision		Revision as of 22:01, 5 November 2009
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	~~== '''Validation of Consensus Run''' ==~~

	=== '''Verification of Consensus Assignments''' ===		=== '''Verification of Consensus Assignments''' ===
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	9.  Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.		9.  Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.

	You may want to run an additional iteration of consensus assignment, though it is usually not necessary.<br>		You may want to run an additional iteration of consensus assignment, though it is usually not necessary.<br>

	=== '''Acceptance Criteria''' ===		=== '''Acceptance Criteria''' ===
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	#The manual run of CYANA structure calculation with distance constraints from consensus assigned NOEs delivers converged structure, the pairwise RMSD of the structure family shall be less than 3A.		#The manual run of CYANA structure calculation with distance constraints from consensus assigned NOEs delivers converged structure, the pairwise RMSD of the structure family shall be less than 3A.
	#The yield of consensus assigned NOEs shall be large than 50%.		#The yield of consensus assigned NOEs shall be large than 50%.

	===		===

Jma: moved ValidationOfConsensusRun to Validation of Consensus Run

2009-11-05T21:58:54Z

moved ValidationOfConsensusRun to Validation of Consensus Run

← Older revision	Revision as of 21:58, 5 November 2009
(No difference)

Jma at 20:45, 4 November 2009

2009-11-04T20:45:15Z

← Older revision		Revision as of 20:45, 4 November 2009
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	2.  Copy consensus peaklists (<tt>n_cons.peaks</tt>, <tt>ali_cons.peaks</tt> and <tt>aro_cons.peaks</tt>) into this subdirectory.		2.  Copy consensus peaklists (<tt>n_cons.peaks</tt>, <tt>ali_cons.peaks</tt> and <tt>aro_cons.peaks</tt>) into this subdirectory.

	If using CARA, re-integrate the peakslist and export them.		If using CARA, re-integrate the peakslist and export them.

	3.  Copy <tt>init.cya</tt>, <tt>XXXX.seq</tt>, <tt>XXXX.prot</tt> and <tt>stereofound.cya</tt> from the CYANA automated run (<tt>cyana21/calc2</tt>). Rename <tt>stereofound.cya</tt> into <tt>stereo.cya</tt>		3.  Copy <tt>init.cya</tt>, <tt>XXXX.seq</tt>, <tt>XXXX.prot</tt> and <tt>stereofound.cya</tt> from the CYANA automated run (<tt>cyana21/calc2</tt>). Rename <tt>stereofound.cya</tt> into <tt>stereo.cya</tt>
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	7.  In CYANA 2.1 run CALC.cya for manual structure calculation with only consensus constraints.		7.  In CYANA 2.1 run CALC.cya for manual structure calculation with only consensus constraints.

	8.  Clean violations the same was is in ~~[[NESG:UsingFOUNDakaHABAS\|~~Verifying Local NOE Network with FOUND (HABAS)]] and try to keep TF < 1.0.		8.  Clean violations the same was is in Verifying Local NOE Network with [[FOUND\|FOUND (HABAS)]] and try to keep TF < 1.0.

	For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY).		For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY).

	Unassign peaks, which appear at spectral artifacts.		Unassign peaks, which appear at spectral artifacts.

	If violation persisit while peak integrals are correct, then modify the calibration parameters.		If violation persisit while peak integrals are correct, then modify the calibration parameters.

	9.  Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.		9.  Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.

Jma at 20:44, 4 November 2009

2009-11-04T20:44:38Z

← Older revision		Revision as of 20:44, 4 November 2009
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	2.  Copy consensus peaklists (<tt>n_cons.peaks</tt>, <tt>ali_cons.peaks</tt> and <tt>aro_cons.peaks</tt>) into this subdirectory.		2.  Copy consensus peaklists (<tt>n_cons.peaks</tt>, <tt>ali_cons.peaks</tt> and <tt>aro_cons.peaks</tt>) into this subdirectory.

	*If using CARA, re-integrate the peakslist and export them.		If using CARA, re-integrate the peakslist and export them.

	3.  Copy <tt>init.cya</tt>, <tt>XXXX.seq</tt>, <tt>XXXX.prot</tt> and <tt>stereofound.cya</tt> from the CYANA automated run (<tt>cyana21/calc2</tt>). Rename <tt>stereofound.cya</tt> into <tt>stereo.cya</tt>		3.  Copy <tt>init.cya</tt>, <tt>XXXX.seq</tt>, <tt>XXXX.prot</tt> and <tt>stereofound.cya</tt> from the CYANA automated run (<tt>cyana21/calc2</tt>). Rename <tt>stereofound.cya</tt> into <tt>stereo.cya</tt>
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	8.  Clean violations the same was is in [[NESG:UsingFOUNDakaHABAS\|Verifying Local NOE Network with FOUND (HABAS)]] and try to keep TF < 1.0.		8.  Clean violations the same was is in [[NESG:UsingFOUNDakaHABAS\|Verifying Local NOE Network with FOUND (HABAS)]] and try to keep TF < 1.0.

	*For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY).		For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY).
	*Unassign peaks, which appear at spectral artifacts.
	*If violation persisit while peak integrals are correct, then modify the calibration parameters.		Unassign peaks, which appear at spectral artifacts.

			If violation persisit while peak integrals are correct, then modify the calibration parameters.

	9.  Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.		9.  Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.

Jma: moved NESG:ValidationOfConsensusRun to ValidationOfConsensusRun

2009-11-04T20:30:45Z

moved NESG:ValidationOfConsensusRun to ValidationOfConsensusRun

← Older revision	Revision as of 20:30, 4 November 2009
(No difference)

Jma at 20:30, 4 November 2009

2009-11-04T20:30:08Z

← Older revision		Revision as of 20:30, 4 November 2009
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	9.  Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.		9.  Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.

	You may want to run an additional iteration of consensus assignment, though it is usually not necessary:		You may want to run an additional iteration of consensus assignment, though it is usually not necessary.<br>
	~~===~~

	=== '''Acceptance Criteria''' ===		=== '''Acceptance Criteria''' ===

Jma at 20:28, 4 November 2009

2009-11-04T20:28:05Z

Jma at 20:26, 4 November 2009

2009-11-04T20:26:56Z

← Older revision		Revision as of 20:26, 4 November 2009
Line 21:		Line 21:
	8.  Clean violations the same was is in [[NESG:UsingFOUNDakaHABAS\|Verifying Local NOE Network with FOUND (HABAS)]] and try to keep TF < 1.0.		8.  Clean violations the same was is in [[NESG:UsingFOUNDakaHABAS\|Verifying Local NOE Network with FOUND (HABAS)]] and try to keep TF < 1.0.

	*For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY).		*For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY).
	*Unassign peaks, which appear at spectral artifacts.		*Unassign peaks, which appear at spectral artifacts.
	*If violation persisit while peak integrals are correct, then modify the calibration parameters.		*If violation persisit while peak integrals are correct, then modify the calibration parameters.

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	==== '''run_caliba.cya''' ====		==== '''run_caliba.cya''' ====
			<pre>protocol:=caliba.log
	<~~nowiki~~>
	protocol:=caliba.log
	read prot $name		read prot $name

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	write upl cons.upl		write upl cons.upl
	protocol:=		protocol:=</pre>
	</~~nowiki~~>

	~~%COMMENT%~~		<br> -- GaohuaLiu - 26 Jan 2007

	~~<br>~~ -- ~~Main.GaohuaLiu~~ - ~~26 Jan 2007~~		-- Edited by JimAramini - Nov 2009

← Older revision		Revision as of 20:28, 4 November 2009
Line 3:		Line 3:
	=== '''Verification of Consensus Assignments''' ===		=== '''Verification of Consensus Assignments''' ===

	1.  Create a working subdirectory, for example, <tt>cyana21/calc2</tt>.		1.  Create a working subdirectory, for example, <tt>cyana21/calc2</tt>.

	2.  Copy consensus peaklists (<tt>n_cons.peaks</tt>, <tt>ali_cons.peaks</tt> and <tt>aro_cons.peaks</tt>) into this subdirectory.		2.  Copy consensus peaklists (<tt>n_cons.peaks</tt>, <tt>ali_cons.peaks</tt> and <tt>aro_cons.peaks</tt>) into this subdirectory.

	*If using CARA, re-integrate the peakslist and export them.		*If using CARA, re-integrate the peakslist and export them.

	3.  Copy <tt>init.cya</tt>, <tt>XXXX.seq</tt>, <tt>XXXX.prot</tt> and <tt>stereofound.cya</tt> from the CYANA automated run (<tt>cyana21/calc2</tt>). Rename <tt>stereofound.cya</tt> into <tt>stereo.cya</tt>		3.  Copy <tt>init.cya</tt>, <tt>XXXX.seq</tt>, <tt>XXXX.prot</tt> and <tt>stereofound.cya</tt> from the CYANA automated run (<tt>cyana21/calc2</tt>). Rename <tt>stereofound.cya</tt> into <tt>stereo.cya</tt>

	4.  Copy <tt>GridSearch.cya</tt>, <tt>CALC.cya</tt> and <tt>talos.aco</tt> from the <tt>found</tt> subdirectory. Modify <tt>GridSearch.cya</tt> to read <tt>cons.upl</tt> instead of <tt>short.upl</tt>.		4.  Copy <tt>GridSearch.cya</tt>, <tt>CALC.cya</tt> and <tt>talos.aco</tt> from the <tt>found</tt> subdirectory. Modify <tt>GridSearch.cya</tt> to read <tt>cons.upl</tt> instead of <tt>short.upl</tt>.

	5.  Create UPL file <tt>cons.upl</tt> using run_caliba.cya (see below).		5.  Create UPL file <tt>cons.upl</tt> using run_caliba.cya (see below).

	6.  In CYANA 2.1 run <tt>GridSearch.cya</tt>		6.  In CYANA 2.1 run <tt>GridSearch.cya</tt>

	7.  In CYANA 2.1 run CALC.cya for manual structure calculation with only consensus constraints.		7.  In CYANA 2.1 run CALC.cya for manual structure calculation with only consensus constraints.

	8.  Clean violations the same was is in [[NESG:UsingFOUNDakaHABAS\|Verifying Local NOE Network with FOUND (HABAS)]] and try to keep TF < 1.0.		8.  Clean violations the same was is in [[NESG:UsingFOUNDakaHABAS\|Verifying Local NOE Network with FOUND (HABAS)]] and try to keep TF < 1.0.

	*For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY).		*For the violated NOE, re-integrate the peaks first if it is overintegrated (in XEASY).
	*Unassign peaks, which appear at spectral artifacts.		*Unassign peaks, which appear at spectral artifacts.
	*If violation persisit while peak integrals are correct, then modify the calibration parameters.		*If violation persisit while peak integrals are correct, then modify the calibration parameters.

	9.  Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.		9.  Verify the additional stereospecific assignments made in this run. Swap the atom groups if needed.

	You may want to run an additional iteration of consensus assignment, though it is usually not necessary:		You may want to run an additional iteration of consensus assignment, though it is usually not necessary:
			===

	=== '''Acceptance Criteria''' ===		=== '''Acceptance Criteria''' ===
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	#The manual run of CYANA structure calculation with distance constraints from consensus assigned NOEs delivers converged structure, the pairwise RMSD of the structure family shall be less than 3A.		#The manual run of CYANA structure calculation with distance constraints from consensus assigned NOEs delivers converged structure, the pairwise RMSD of the structure family shall be less than 3A.
	#The yield of consensus assigned NOEs shall be large than 50%.		#The yield of consensus assigned NOEs shall be large than 50%.
			===

	=== '''Example scripts''' ===		=== '''Example scripts''' ===
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	write upl cons.upl		write upl cons.upl
	protocol:=</pre>		protocol:=</pre>
			<br> <br> -- GaohuaLiu - 26 Jan 2007

	<br> -- GaohuaLiu - 26 Jan 2007

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