XEASY Backbone Assignment - Revision history

Jlmills: Blanked the page

2009-11-24T20:18:54Z

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Agutmana at 22:01, 11 November 2009

2009-11-11T22:01:28Z

← Older revision		Revision as of 22:01, 11 November 2009
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	*'''validate_assignments.pl''' - performs a statistical evaluation of assigned chemical shifts in a BMRB file. <br> Usage: validate_assignments.pl [options] input_bmrb_file <br>		*'''validate_assignments.pl''' - performs a statistical evaluation of assigned chemical shifts in a BMRB file. <br> Usage: validate_assignments.pl [options] input_bmrb_file <br>
	*'''typing_degeneracy.pl''' - performs a statistical evaluation on the uniqueness of the protein sequence and the uniqueness of mapped segments of spin systems. <br> Usage: typing_degeneracy.pl [options] <br>		*'''typing_degeneracy.pl''' - performs a statistical evaluation on the uniqueness of the protein sequence and the uniqueness of mapped segments of spin systems. <br> Usage: typing_degeneracy.pl [options] <br>
	*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html ~~Broken link~~] for more detail.		*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html] for more detail.

	<br> -- Main.GaohuaLiu - 04 Feb 2007 files for download:		<br> -- Main.GaohuaLiu - 04 Feb 2007 files for download:

Agutmana at 22:00, 11 November 2009

2009-11-11T22:00:38Z

← Older revision		Revision as of 22:00, 11 November 2009
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	*'''validate_assignments.pl''' - performs a statistical evaluation of assigned chemical shifts in a BMRB file. <br> Usage: validate_assignments.pl [options] input_bmrb_file <br>		*'''validate_assignments.pl''' - performs a statistical evaluation of assigned chemical shifts in a BMRB file. <br> Usage: validate_assignments.pl [options] input_bmrb_file <br>
	*'''typing_degeneracy.pl''' - performs a statistical evaluation on the uniqueness of the protein sequence and the uniqueness of mapped segments of spin systems. <br> Usage: typing_degeneracy.pl [options] <br>		*'''typing_degeneracy.pl''' - performs a statistical evaluation on the uniqueness of the protein sequence and the uniqueness of mapped segments of spin systems. <br> Usage: typing_degeneracy.pl [options] <br>
	*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html\|Broken link] for more detail.		*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html Broken link] for more detail.

	<br> -- Main.GaohuaLiu - 04 Feb 2007 files for download:		<br> -- Main.GaohuaLiu - 04 Feb 2007 files for download:

Agutmana at 22:00, 11 November 2009

2009-11-11T22:00:10Z

← Older revision		Revision as of 22:00, 11 November 2009
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	*'''validate_assignments.pl''' - performs a statistical evaluation of assigned chemical shifts in a BMRB file. <br> Usage: validate_assignments.pl [options] input_bmrb_file <br>		*'''validate_assignments.pl''' - performs a statistical evaluation of assigned chemical shifts in a BMRB file. <br> Usage: validate_assignments.pl [options] input_bmrb_file <br>
	*'''typing_degeneracy.pl''' - performs a statistical evaluation on the uniqueness of the protein sequence and the uniqueness of mapped segments of spin systems. <br> Usage: typing_degeneracy.pl [options] <br>		*'''typing_degeneracy.pl''' - performs a statistical evaluation on the uniqueness of the protein sequence and the uniqueness of mapped segments of spin systems. <br> Usage: typing_degeneracy.pl [options] <br>
	*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/~~cmap image editor~~.html\|Broken link] for more detail.		*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html\|Broken link] for more detail.

	<br> -- Main.GaohuaLiu - 04 Feb 2007 files for download:		<br> -- Main.GaohuaLiu - 04 Feb 2007 files for download:

Agutmana at 21:59, 11 November 2009

2009-11-11T21:59:30Z

← Older revision		Revision as of 21:59, 11 November 2009
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	*'''validate_assignments.pl''' - performs a statistical evaluation of assigned chemical shifts in a BMRB file. <br> Usage: validate_assignments.pl [options] input_bmrb_file <br>		*'''validate_assignments.pl''' - performs a statistical evaluation of assigned chemical shifts in a BMRB file. <br> Usage: validate_assignments.pl [options] input_bmrb_file <br>
	*'''typing_degeneracy.pl''' - performs a statistical evaluation on the uniqueness of the protein sequence and the uniqueness of mapped segments of spin systems. <br> Usage: typing_degeneracy.pl [options] <br>		*'''typing_degeneracy.pl''' - performs a statistical evaluation on the uniqueness of the protein sequence and the uniqueness of mapped segments of spin systems. <br> Usage: typing_degeneracy.pl [options] <br>
	*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap image editor.html\|~~http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html~~] for more detail.		*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap image editor.html\|Broken link] for more detail.

	<br> -- Main.GaohuaLiu - 04 Feb 2007 files for download:		<br> -- Main.GaohuaLiu - 04 Feb 2007 files for download:

Agutmana at 21:58, 11 November 2009

2009-11-11T21:58:10Z

← Older revision		Revision as of 21:58, 11 November 2009
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	=== '''Assignment Validation''' ===		=== '''Assignment Validation''' ===

	Once the assignment results were obtained from, it is required to validate the assignments. AutoAssign provides Assignment Validation Software suite (AVS) to aid the user in validating assignments. Please check the [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/tutorial.html ~~AutoAssign Tutorial~~] for detailed usage. The four main tools in AVS are:		Once the assignment results were obtained from, it is required to validate the assignments. AutoAssign provides Assignment Validation Software suite (AVS) to aid the user in validating assignments. Please check the AutoAssign Tutorial at [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/tutorial.html http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/tutorial.html] for detailed usage. The four main tools in AVS are:

	*'''missing_shifts.pl''' - shows which shifts in a BMRB file are missing and statistics on assignment completeness. <br> Usage: missing_shifts.pl [ options ] input_bmrb_file <br>		*'''missing_shifts.pl''' - shows which shifts in a BMRB file are missing and statistics on assignment completeness. <br> Usage: missing_shifts.pl [ options ] input_bmrb_file <br>
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	*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap image editor.html\|http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html] for more detail.		*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap image editor.html\|http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html] for more detail.

			<br> -- Main.GaohuaLiu - 04 Feb 2007 files for download:

	~~-- Main~~.~~GaohuaLiu - 04 Feb 2007 files for download~~:		*[[Media:XEASY_makeCabcaPeak.txt\|makeCabcaPeak]]: makeCabcaPeak

	*[[Media:~~XEASY makeCabcaPeak~~.txt\|~~makeCabcaPeak~~]]: ~~makeCabcaPeak~~		*[[Media:XEASY_makeBbNNoesy.txt\|makeBbNNoesy]]: makeBbNNoesy

	*[[Media:~~XEASY makeBbNNoesy~~.txt\|~~makeBbNNoesy~~]]: ~~makeBbNNoesy~~		*[[Media:XEASY_AA2Xeasy.txt\|AA2Xeasy]]: AA2Xeasy

	*[[Media:~~XEASY AA2Xeasy~~.txt\|~~AA2Xeasy~~]]: ~~AA2Xeasy~~		*[[Media:XEASY_makeAutoList.txt\|makeAutoList]]: makeAutoList

	*[[Media:~~XEASY makeAutoList~~.~~txt~~\|~~makeAutoList~~]]: ~~makeAutoList~~		*[[Media:XEASY_myprot.aat\|myprot.aat]]: myprot.aat

	*[[Media:~~XEASY myprot.aat\|myprot.aat]]: myprot.aat~~		*[[Media:XEASY_autos_README.txt\|autos_README]]: autos_README

	*[[Media:XEASY autos README.txt\|autos_README]]: autos_README

Agutmana at 21:57, 11 November 2009

2009-11-11T21:57:14Z

← Older revision		Revision as of 21:57, 11 November 2009
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	=== '''Use Of 15N-resolved [1H,1H] NOESY Spectrum''' ===		=== '''Use Of 15N-resolved [1H,1H] NOESY Spectrum''' ===

	Sequential NOEs observed in 15N-resolved [1H,1H] NOESY Spectrum can be used to confirm and facilitate backbone assignment. A convinient way is described here on how to do the sequential assignment by using the 15N-resolved [1H,1H] NOESY spectrum. Please check section '''Confirming Backbone Assignment from AutoAssign in XEASY''', [Complete Backbone Assignment by ~~perform~~ sequential ordering of SRDs and [[~~NESG:~~Side Chain Assignment\|Side Chain Assignment]] for addtional ~~and other~~ informations.		Sequential NOEs observed in 15N-resolved [1H,1H] NOESY Spectrum can be used to confirm and facilitate backbone assignment. A convinient way is described here on how to do the sequential assignment by using the 15N-resolved [1H,1H] NOESY spectrum. Please check section '''Confirming Backbone Assignment from AutoAssign in XEASY''', Complete Backbone Assignment by performing sequential ordering of SRDs and [[Side Chain Assignment in XEASY\|Side Chain Assignment]] for addtional informations.

	#In UBNMR, run <tt>makeBbNNoesy</tt> to use the 15N /1HN backbone shifts of SRD-I to generate a starting peaklist that only contains diagonal peaks for analysis of the 15N-resolved part of simultaneous 3D 15N/13Caliphatic/13Caromatic-resolved [1H,1H]-NOESY.		#In UBNMR, run <tt>makeBbNNoesy</tt> to use the 15N /1HN backbone shifts of SRD-I to generate a starting peaklist that only contains diagonal peaks for analysis of the 15N-resolved part of simultaneous 3D 15N/13Caliphatic/13Caromatic-resolved [1H,1H]-NOESY.
	#In XEASY, use <tt>ns</tt> to load 15N-resolved NOESY; use <tt>ls</tt> to load the SequenceList; use <tt>lp</tt> to load the corresponding starting peak list. There is no need to move any peaks at this time.		#In XEASY, use <tt>ns</tt> to load 15N-resolved NOESY; use <tt>ls</tt> to load the SequenceList; use <tt>lp</tt> to load the corresponding starting peak list. There is no need to move any peaks at this time.
	#In XEASY, use <tt>cd</tt> and <tt>cc</tt> to find sequential connectivities in 15N-resolved NOESY.		#In XEASY, use <tt>cd</tt> and <tt>cc</tt> to find sequential connectivities in 15N-resolved NOESY.
	##After generating a strip list, type <tt>cd</tt> to calculated the the correlation coefficient between every two strips. <tt>he [cd</tt> command produces a pop-up window with the default values shown below. <br> '''Figure 3. The pop-up window after command <tt>cd</tt>.''' <br> [[~~File~~:~~XEASY_cd~~.jpg]] <br> <br> Please see the Xeasy manual for specifics regarding these parameters. The default parameters are sufficient for 15N resolved [1H, 1H]-NOESY. For searching other spectra (triple resonance, etc.) the "Factor to enhance peaks" and "Factor to reduce peaks" should both be set to "1.0 1.0". The choices for inter- and intra-spectral searches and "use absolute intensities" should also be considered.		##After generating a strip list, type <tt>cd</tt> to calculated the the correlation coefficient between every two strips. <tt>he [cd</tt> command produces a pop-up window with the default values shown below. <br> '''Figure 3. The pop-up window after command <tt>cd</tt>.''' <br> [[Image:XEASY cd.jpg]] <br> <br> Please see the Xeasy manual for specifics regarding these parameters. The default parameters are sufficient for 15N resolved [1H, 1H]-NOESY. For searching other spectra (triple resonance, etc.) the "Factor to enhance peaks" and "Factor to reduce peaks" should both be set to "1.0 1.0". The choices for inter- and intra-spectral searches and "use absolute intensities" should also be considered.
	##Use <tt>gs</tt>, <tt>sf</tt>, <tt>sf</tt> or <tt>bf</tt> to display the intersted strip on the screen.		##Use <tt>gs</tt>, <tt>sf</tt>, <tt>sf</tt> or <tt>bf</tt> to display the intersted strip on the screen.
	##Typing <tt>cc</tt>, then click on any position in the strip interested. Xeasy will then sort all strips according to the correlation coifficients of these strips to the clicked strips. The strips sequential residues often give the highest correlation coifficients and can be easily identified in this way. The identified sequential residues need to be confirmed from the triple resonance spectra.		##Typing <tt>cc</tt>, then click on any position in the strip interested. Xeasy will then sort all strips according to the correlation coifficients of these strips to the clicked strips. The strips sequential residues often give the highest correlation coifficients and can be easily identified in this way. The identified sequential residues need to be confirmed from the triple resonance spectra.

Agutmana at 21:55, 11 November 2009

2009-11-11T21:55:15Z

← Older revision		Revision as of 21:55, 11 November 2009
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	# Maually checking results from AutoAssign and completing the assignment.<br/>		# Maually checking results from AutoAssign and completing the assignment.<br/>

	=== '''Use Of 15N-resolved [1H,1H] NOESY Spectrum''' ===		=== '''Use Of 15N-resolved [1H,1H] NOESY Spectrum''' ===

	Sequential NOEs observed in 15N-resolved [1H,1H] NOESY Spectrum can be used to confirm and facilitate backbone assignment. A convinient way is described here on how to do the sequential assignment by using the 15N-resolved [1H,1H] NOESY spectrum. Please check section '''Confirming Backbone Assignment from AutoAssign in XEASY''', [Complete Backbone Assignment by perform sequential ordering of SRDs and [[NESG:Side Chain Assignment\|Side Chain Assignment]] for addtional and other informations.		Sequential NOEs observed in 15N-resolved [1H,1H] NOESY Spectrum can be used to confirm and facilitate backbone assignment. A convinient way is described here on how to do the sequential assignment by using the 15N-resolved [1H,1H] NOESY spectrum. Please check section '''Confirming Backbone Assignment from AutoAssign in XEASY''', [Complete Backbone Assignment by perform sequential ordering of SRDs and [[NESG:Side Chain Assignment\|Side Chain Assignment]] for addtional and other informations.
	# In UBNMR, run <tt>makeBbNNoesy</tt> to use the 15N /1HN backbone shifts of SRD-I to generate a starting peaklist that only contains diagonal peaks for analysis of the 15N-resolved part of simultaneous 3D 15N/13Caliphatic/13Caromatic-resolved [1H,1H]-NOESY.
	# In XEASY, use <tt>ns</tt> to load 15N-resolved NOESY; use <tt>ls</tt> to load the SequenceList; use <tt>lp</tt> to load the corresponding starting peak list. There is no need to move any peaks at this time.
	~~# In XEASY, use <tt>cd</tt> and <tt>cc</tt> to find sequential connectivities in 15N-resolved NOESY.~~
	## After generating a strip list, type <tt>cd</tt> to calculated the the correlation coefficient between every two strips. <tt>he [cd</tt> command produces a pop-up window with the default values shown below. <br/> '''Figure 3. The pop-up window after command <tt>cd</tt>.''' <br /> <img src="%ATTACHURLPATH%/cd.jpg" alt="cd.jpg" width='390' height='282' /> <br /> <br /> Please see the Xeasy manual for specifics regarding these parameters. The default parameters are sufficient for 15N resolved [1H, 1H]-NOESY. For searching other spectra (triple resonance, etc.) the "Factor to enhance peaks" and "Factor to reduce peaks" should both be set to "1.0 1.0". The choices for inter- and intra-spectral searches and "use absolute intensities" should also be considered.
	~~## Use <tt>gs</tt>, <tt>sf</tt>, <tt>sf</tt> or <tt>bf</tt> to display the intersted strip on the screen.~~
	## Typing <tt>cc</tt>, then click on any position in the strip interested. Xeasy will then sort all strips according to the correlation coifficients of these strips to the clicked strips. The strips sequential residues often give the highest correlation coifficients and can be easily identified in this way. The identified sequential residues need to be confirmed from the triple resonance spectra.


			#In UBNMR, run <tt>makeBbNNoesy</tt> to use the 15N /1HN backbone shifts of SRD-I to generate a starting peaklist that only contains diagonal peaks for analysis of the 15N-resolved part of simultaneous 3D 15N/13Caliphatic/13Caromatic-resolved [1H,1H]-NOESY.
			#In XEASY, use <tt>ns</tt> to load 15N-resolved NOESY; use <tt>ls</tt> to load the SequenceList; use <tt>lp</tt> to load the corresponding starting peak list. There is no need to move any peaks at this time.
			#In XEASY, use <tt>cd</tt> and <tt>cc</tt> to find sequential connectivities in 15N-resolved NOESY.
			##After generating a strip list, type <tt>cd</tt> to calculated the the correlation coefficient between every two strips. <tt>he [cd</tt> command produces a pop-up window with the default values shown below. <br> '''Figure 3. The pop-up window after command <tt>cd</tt>.''' <br> [[File:XEASY_cd.jpg]] <br> <br> Please see the Xeasy manual for specifics regarding these parameters. The default parameters are sufficient for 15N resolved [1H, 1H]-NOESY. For searching other spectra (triple resonance, etc.) the "Factor to enhance peaks" and "Factor to reduce peaks" should both be set to "1.0 1.0". The choices for inter- and intra-spectral searches and "use absolute intensities" should also be considered.
			##Use <tt>gs</tt>, <tt>sf</tt>, <tt>sf</tt> or <tt>bf</tt> to display the intersted strip on the screen.
			##Typing <tt>cc</tt>, then click on any position in the strip interested. Xeasy will then sort all strips according to the correlation coifficients of these strips to the clicked strips. The strips sequential residues often give the highest correlation coifficients and can be easily identified in this way. The identified sequential residues need to be confirmed from the triple resonance spectra.

	=== '''Assignment Validation''' ===		=== '''Assignment Validation''' ===

Agutmana at 21:53, 11 November 2009

2009-11-11T21:53:38Z

← Older revision		Revision as of 21:53, 11 November 2009
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	=== '''Assignment Validation''' ===		=== '''Assignment Validation''' ===

	Once the assignment results were obtained from, it is required to validate the assignments. AutoAssign provides Assignment Validation Software suite (AVS) to aid the user in validating assignments. Please check the [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/tutorial.html AutoAssign Tutorial] for detailed usage. The four main tools in AVS are:		Once the assignment results were obtained from, it is required to validate the assignments. AutoAssign provides Assignment Validation Software suite (AVS) to aid the user in validating assignments. Please check the [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/tutorial.html AutoAssign Tutorial] for detailed usage. The four main tools in AVS are:
	* '''missing_shifts.pl''' - shows which shifts in a BMRB file are missing and statistics on assignment completeness. <br/> Usage: missing_shifts.pl [ options ] input_bmrb_file <br/>
	* '''validate_assignments.pl''' - performs a statistical evaluation of assigned chemical shifts in a BMRB file. <br/> Usage: validate_assignments.pl [options] input_bmrb_file <br/>
	* '''typing_degeneracy.pl''' - performs a statistical evaluation on the uniqueness of the protein sequence and the uniqueness of mapped segments of spin systems. <br/> Usage: typing_degeneracy.pl [options] <br/>
	* '''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [[NESG:http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html\|http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html]] for more detail.

			*'''missing_shifts.pl''' - shows which shifts in a BMRB file are missing and statistics on assignment completeness. <br> Usage: missing_shifts.pl [ options ] input_bmrb_file <br>
			*'''validate_assignments.pl''' - performs a statistical evaluation of assigned chemical shifts in a BMRB file. <br> Usage: validate_assignments.pl [options] input_bmrb_file <br>
			*'''typing_degeneracy.pl''' - performs a statistical evaluation on the uniqueness of the protein sequence and the uniqueness of mapped segments of spin systems. <br> Usage: typing_degeneracy.pl [options] <br>
			*'''CMap Image Editor''' - generates graphical representations of a protein's resonance assignments and all data supporting the assignments. Please check [http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap image editor.html\|http://www-nmr.cabm.rutgers.edu/NMRsoftware/autoassign/Documentation/Help/cmap_image_editor.html] for more detail.

	~~%COMMENT%~~
	<span class="commentPlugin commentPluginOutputOneliner"> * Gaohua, where can i find the makeBbNNoesy script for UBNMR? it is not on the directory tree, or in the scripts directory. Are there other scripts here that are not being used anymore? thanks! -- Main.AnaZeri - 29 Aug 2007 - 09:45</span></span><!--/commentPlugin-->
	<span class="commentPlugin commentPluginOutputOneliner"> * Gaohua, the script A2NeSGC.XEASY is not working, and the guys here at Buffalo use a different one, updatemapping. what shall we do about this? Thanks, Ana -- Main.AnaZeri - 28 Aug 2007 - 11:41</span></span><!--/commentPlugin-->

	-- Main.GaohuaLiu - 04 Feb 2007		-- Main.GaohuaLiu - 04 Feb 2007 files for download:
	files for download:

	* [[~~NESG~~:~~%ATTACHURL%/~~makeCabcaPeak\|makeCabcaPeak]]: makeCabcaPeak		*[[Media:XEASY makeCabcaPeak.txt\|makeCabcaPeak]]: makeCabcaPeak

	* [[~~NESG~~:~~%ATTACHURL%/~~makeBbNNoesy\|makeBbNNoesy]]: makeBbNNoesy		*[[Media:XEASY makeBbNNoesy.txt\|makeBbNNoesy]]: makeBbNNoesy

	* [[~~NESG~~:~~%ATTACHURL%/~~AA2Xeasy\|AA2Xeasy]]: AA2Xeasy		*[[Media:XEASY AA2Xeasy.txt\|AA2Xeasy]]: AA2Xeasy

	* [[~~NESG~~:~~%ATTACHURL%/~~makeAutoList\|makeAutoList]]: makeAutoList		*[[Media:XEASY makeAutoList.txt\|makeAutoList]]: makeAutoList

	* [[~~NESG~~:~~%ATTACHURL%/~~myprot.aat\|myprot.aat]]: myprot.aat		*[[Media:XEASY myprot.aat\|myprot.aat]]: myprot.aat

	* [[~~NESG~~:~~%ATTACHURL%/autos_README~~\|autos_README]]: autos_README		*[[Media:XEASY autos README.txt\|autos_README]]: autos_README

Agutmana at 21:51, 11 November 2009

2009-11-11T21:51:04Z

← Older revision		Revision as of 21:51, 11 November 2009
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	##In XEASY, use <tt>ns</tt>, <tt>ls</tt>, <tt>lc</tt>, and <tt>lp</tt> to load HNNCABCA and CABCA(CO)NHN spectra and the SequenceList, ProtonList and PeakList; use <tt>se</tt>, <tt>gs</tt>, <tt>fs</tt> and <tt>bs</tt> to sort and display strips (Figure 1A); use <tt>mr</tt> to identify and move peaks (Figure 1B); start with CABCA(CO)NHN sub-spectra and continue with HNNCABCA sub-spectra (remove unobserved peaks); use <tt>ra</tt> regularly to check on the quality of the PeakList; <tt>ac</tt>, <tt>wc</tt> and <tt>wp</tt> to save updated lists. <br> <br> '''Figure 1: Peak picking of (4,3)D GFT HNNCABCA and CABCA(CO)NHN spectra.''' <br> '''A: Before peak position adjustment by <tt>mr</tt>;''' <br> [[Image:XEASY backbone1.jpg]] <br> <br> '''B: After peak position adjustment by <tt>mr</tt>.''' <br> [[Image:XEASY backbone2.jpg]] <br> <br>		##In XEASY, use <tt>ns</tt>, <tt>ls</tt>, <tt>lc</tt>, and <tt>lp</tt> to load HNNCABCA and CABCA(CO)NHN spectra and the SequenceList, ProtonList and PeakList; use <tt>se</tt>, <tt>gs</tt>, <tt>fs</tt> and <tt>bs</tt> to sort and display strips (Figure 1A); use <tt>mr</tt> to identify and move peaks (Figure 1B); start with CABCA(CO)NHN sub-spectra and continue with HNNCABCA sub-spectra (remove unobserved peaks); use <tt>ra</tt> regularly to check on the quality of the PeakList; <tt>ac</tt>, <tt>wc</tt> and <tt>wp</tt> to save updated lists. <br> <br> '''Figure 1: Peak picking of (4,3)D GFT HNNCABCA and CABCA(CO)NHN spectra.''' <br> '''A: Before peak position adjustment by <tt>mr</tt>;''' <br> [[Image:XEASY backbone1.jpg]] <br> <br> '''B: After peak position adjustment by <tt>mr</tt>.''' <br> [[Image:XEASY backbone2.jpg]] <br> <br>
	#'''Initial Backbone Assignment from AutoAssign''' <br>		#'''Initial Backbone Assignment from AutoAssign''' <br>
	##Go to <tt>/analysis/xeasy/backbone/autos</tt>, read file [[Media:XEASY_autos_README.txt\|autos_README]] for instructions on how to edit the macro [[Media:XEASY_makeAutoList.txt\|makeAutoList]] and file <tt>myprot.aat</tt>. In UBNMR run <tt>makeAutoList</tt> to generate input files for AutoAssign. Erros at this step can be corrected by looking closely at the peaks reported, moving them again if needed, and running UBNMR makeAutoList again, until all erros are eliminated. The peak ID of one simulated AutoAssign input file ('''myprot-hsqc.pks''') correspond to the residue number of '''SRD-I''', which is required for this protocol. <br> '''Since HNNCABCA and CABCA(CO)NHN spectra provide 4D information, it is suggested that generate the 4D peak list for AutoAssign in order to take full advantage of GFT spectra and get a better assignment results.'''		##Go to <tt>/analysis/xeasy/backbone/autos</tt>, read file [[Media:XEASY_autos_README.txt\|autos_README]] for instructions on how to edit the macro [[Media:XEASY_makeAutoList.txt\|makeAutoList]] and file <tt>myprot.aat</tt>. In UBNMR run <tt>makeAutoList</tt> to generate input files for AutoAssign. Erros at this step can be corrected by looking closely at the peaks reported, moving them again if needed, and running UBNMR makeAutoList again, until all erros are eliminated. The peak ID of one simulated AutoAssign input file ('''myprot-hsqc.pks''') correspond to the residue number of '''SRD-I''', which is required for this protocol. <br> '''Since HNNCABCA and CABCA(CO)NHN spectra provide 4D information, it is suggested that generate the 4D peak list for AutoAssign in order to take full advantage of GFT spectra and get a better assignment results.'''
	##*Click for the AutoAssign control file example [[Media:XEASY_myprot.aat\|myprot.aat]].		##*Click for the AutoAssign control file example [[Media:XEASY_myprot.aat\|myprot.aat]].
	##*Peak pattern used in the AutoAssign input file of 3D CACB type experiments: HN(i), N(i), CA(i or i-1) or CB(i or i-1);		##*Peak pattern used in the AutoAssign input file of 3D CACB type experiments: HN(i), N(i), CA(i or i-1) or CB(i or i-1);
	##*Peak pattern used in the AutoAssign input file of 4D CACB type experiments: HN(i), N(i), CA(i), CA(i) or CB(i); and HN(i), N(i), CA(i-1), CA(i-1) or CB(i-1).<br>		##*Peak pattern used in the AutoAssign input file of 4D CACB type experiments: HN(i), N(i), CA(i), CA(i) or CB(i); and HN(i), N(i), CA(i-1), CA(i-1) or CB(i-1).<br>
	##Run AutoAssign several times with varying matching tolerances for CA and CB in the myprot.aat file (0.1-0.6ppm); save AutoAssign output files;<br>		##Run AutoAssign several times with varying matching tolerances for CA and CB in the myprot.aat file (0.1-0.6ppm); save AutoAssign output files;<br>
	##*It is suggested to use <tt>Default Execution</tt> method to run the program.		##*It is suggested to use <tt>Default Execution</tt> method to run the program.
	##*From the main menu of AutoAssign, follow option <tt>Examine</tt> > <tt>All GSs</tt> to write output file that contains both AutoAssign assignment and the corresponding '''SRD-I''' residue numbers. <br>		##*From the main menu of AutoAssign, follow option <tt>Examine</tt> > <tt>All GSs</tt> to write output file that contains both AutoAssign assignment and the corresponding '''SRD-I''' residue numbers. <br>
	##In UBNMR, run macro [[Media:XEASY_AA2Xeasy.txt\|AA2Xeasy]] to use the best or consensus AutoAssign output file to complement the SRD-I and SRD-II entries of the XEASY SequenceList with <tt>mapping numbers</tt>. <br> <br>		##In UBNMR, run macro [[Media:XEASY_AA2Xeasy.txt\|AA2Xeasy]] to use the best or consensus AutoAssign output file to complement the SRD-I and SRD-II entries of the XEASY SequenceList with <tt>mapping numbers</tt>. <br> <br>

	<br> Modified macro for AA2XEASY		<br> Modified macro for AA2XEASY
	<pre>#UBNMR script for converting autoassign results to xeasy format sequence		<blockquote><pre>#UBNMR script for converting autoassign results to xeasy format sequence

	init		init
Line 40:		Line 40:

	write sequence aa.seq		write sequence aa.seq
	</pre>		</pre></blockquote>
	<br>		<br>

Line 60:		Line 60:
	##In XEASY, use <tt>aa</tt>, <tt>ac</tt>, <tt>ws</tt>, <tt>wc</tt> and <tt>wp</tt> to save all XEASY files before switching from SRD to sequential amino acid residue numbering using <tt>sn</tt>. This yields modified SequenceList, AtomList and PeakList which should be saved, and re-loaded and saved a second time.		##In XEASY, use <tt>aa</tt>, <tt>ac</tt>, <tt>ws</tt>, <tt>wc</tt> and <tt>wp</tt> to save all XEASY files before switching from SRD to sequential amino acid residue numbering using <tt>sn</tt>. This yields modified SequenceList, AtomList and PeakList which should be saved, and re-loaded and saved a second time.
	##In UBNMR, run <tt>cleanBbGftProt</tt> to make a clean AtomList and SeqList by deleting extra atoms and SRDs, fixing nomenclature, and updating single-quantum 13CA and 13CA shifts.		##In UBNMR, run <tt>cleanBbGftProt</tt> to make a clean AtomList and SeqList by deleting extra atoms and SRDs, fixing nomenclature, and updating single-quantum 13CA and 13CA shifts.
	<pre>#UBNMR macro cleanBbGftProt		<blockquote><pre>#UBNMR macro cleanBbGftProt

	init		init
Line 79:		Line 79:

	write prot final-clean.prot		write prot final-clean.prot
	</pre>		</pre></blockquote>

	=== '''Analysis of the(4,2)D GFTHNNCABCA and CABCA(CO)NHN Spectra''' ===		=== '''Analysis of the(4,2)D GFTHNNCABCA and CABCA(CO)NHN Spectra''' ===