Resonance Assignment/Sparky - Revision history

Agutmana: moved Sparky to Resonance Assignment/Sparky

2010-01-05T23:22:49Z

moved Sparky to Resonance Assignment/Sparky

← Older revision	Revision as of 23:22, 5 January 2010
(No difference)

Jma at 16:54, 5 January 2010

2010-01-05T16:54:06Z

← Older revision		Revision as of 16:54, 5 January 2010
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	Sparky is a software package developed at the University of San Francisco for visualizing and analyzing multidimensional (2D, 3D or 4D) NMR spectra.  Sparky plays a critical role as the link between spectral data and assignment/structure determination programs.  The input for the program is processed spectra from various formats (NMRPipe, Felix, Varian or Bruker) converted into Sparky (i.e., “ucsf” format) via processing scripts supplied with the program.  One can output a variety of data from Sparky including:  chemical shift assignments, peak lists, and post script images of spectra.   In the following sections we describe the practical aspects of using Sparky and standard approaches employed by NESG researchers using this program in structure determination projects.  A descriptive on-line manual for a recent Sparky version (3.115) is available at: [http://www.cgl.ucsf.edu/home/sparky/manual/index.html www.cgl.ucsf.edu/home/sparky/manual/index.html].		Sparky is a software package developed at the University of San Francisco for visualizing and analyzing multidimensional (2D, 3D or 4D) NMR spectra.  Sparky plays a critical role as the link between spectral data and assignment/structure determination programs.  The input for the program is processed spectra from various formats (NMRPipe, Felix, Varian or Bruker) converted into Sparky (i.e., “ucsf” format) via processing scripts supplied with the program.  One can output a variety of data from Sparky including:  chemical shift assignments, peak lists, and post script images of spectra.   In the following sections we describe the practical aspects of using Sparky and standard approaches employed by NESG researchers using this program in structure determination projects.  A descriptive on-line manual for a recent Sparky version (3.115) is available at: [http://www.cgl.ucsf.edu/home/sparky/manual/index.html www.cgl.ucsf.edu/home/sparky/manual/index.html].



	== '''Methods''' ==		== '''Methods''' ==
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	[[Image:Sparky Fig6b.png\|800x500px]]		[[Image:Sparky Fig6b.png\|800x500px]]

	c.  Preparation of final bmrb file<br>For the most precise chemical shifts it is recommended that a final resonance list file (made by “rl”) be generated based on a subset of assigned spectra (2D NH-HSQC, 2D CH-HSQC aliphatic and aromatic, 3D HNCO and 3D HN(CA)CO; alternatively, the carbonyl spectra can be omitted and those assignments can be added to the bmrb file later). If one begins from a larger project and deletes other spectra, use the “dr” command to delete any unused assignments.  Also, try to avoid using “Q” in your assignment nomenclature in this subset of spectra.  Check the standard deviations in the resonance list for any unusually high values, to be sure there are no incorrect assignments.  This resonance list is then converted to a bmrb using the “sparkyRL2bmrb.pl” script as described above. Prior to moving on to structure determination programs, it is advisable to check the bmrb file for any missing or unusual shifts/typos using the AVS scripts, “missing_shifts.pl” and “validate_assignments.pl”. <br>		c.  Preparation of final bmrb file<br>For the most precise chemical shifts it is recommended that a final resonance list file (made by “rl”) be generated based on a subset of assigned spectra (2D NH-HSQC, 2D CH-HSQC aliphatic and aromatic, 3D HNCO and 3D HN(CA)CO; alternatively, the carbonyl spectra can be omitted and those assignments can be added to the bmrb file later). If one begins from a larger project and deletes other spectra, use the “dr” command to delete any unused assignments.  Also, try to avoid using “Q” in your assignment nomenclature in this subset of spectra.  Check the standard deviations in the resonance list for any unusually high values, to be sure there are no incorrect assignments.  This resonance list is then converted to a bmrb using the “sparkyRL2bmrb.pl” script as described above. Prior to moving on to structure determination programs, it is advisable to check the bmrb file for any missing or unusual shifts/typos using the AVS scripts, “missing_shifts.pl” and “validate_assignments.pl”. <br>

	== '''References''' ==		== '''References''' ==
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	<br>		<br>

	~~-- Jim Aramini - 27 October 2009~~<br> <br> <br>		<br> <br> <br>

	<br>		<br>

Jma at 18:29, 3 November 2009

2009-11-03T18:29:38Z

← Older revision		Revision as of 18:29, 3 November 2009
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	c.  Preparation of final bmrb file<br>For the most precise chemical shifts it is recommended that a final resonance list file (made by “rl”) be generated based on a subset of assigned spectra (2D NH-HSQC, 2D CH-HSQC aliphatic and aromatic, 3D HNCO and 3D HN(CA)CO; alternatively, the carbonyl spectra can be omitted and those assignments can be added to the bmrb file later). If one begins from a larger project and deletes other spectra, use the “dr” command to delete any unused assignments.  Also, try to avoid using “Q” in your assignment nomenclature in this subset of spectra.  Check the standard deviations in the resonance list for any unusually high values, to be sure there are no incorrect assignments.  This resonance list is then converted to a bmrb using the “sparkyRL2bmrb.pl” script as described above. Prior to moving on to structure determination programs, it is advisable to check the bmrb file for any missing or unusual shifts/typos using the AVS scripts, “missing_shifts.pl” and “validate_assignments.pl”. <br>		c.  Preparation of final bmrb file<br>For the most precise chemical shifts it is recommended that a final resonance list file (made by “rl”) be generated based on a subset of assigned spectra (2D NH-HSQC, 2D CH-HSQC aliphatic and aromatic, 3D HNCO and 3D HN(CA)CO; alternatively, the carbonyl spectra can be omitted and those assignments can be added to the bmrb file later). If one begins from a larger project and deletes other spectra, use the “dr” command to delete any unused assignments.  Also, try to avoid using “Q” in your assignment nomenclature in this subset of spectra.  Check the standard deviations in the resonance list for any unusually high values, to be sure there are no incorrect assignments.  This resonance list is then converted to a bmrb using the “sparkyRL2bmrb.pl” script as described above. Prior to moving on to structure determination programs, it is advisable to check the bmrb file for any missing or unusual shifts/typos using the AVS scripts, “missing_shifts.pl” and “validate_assignments.pl”. <br>

	== '''~~Reference~~''' ==		== '''References''' ==

	When using Sparky in your structure determination please cite:<br>    T.D. Goddard & D.G. Kneller, SPARKY 3,<br>    University of California, San Francisco<br>		When using Sparky in your structure determination please cite:<br>    T.D. Goddard & D.G. Kneller, SPARKY 3,<br>    University of California, San Francisco<br>

Jma at 18:29, 3 November 2009

2009-11-03T18:29:12Z

← Older revision		Revision as of 18:29, 3 November 2009
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	c.  Preparation of final bmrb file<br>For the most precise chemical shifts it is recommended that a final resonance list file (made by “rl”) be generated based on a subset of assigned spectra (2D NH-HSQC, 2D CH-HSQC aliphatic and aromatic, 3D HNCO and 3D HN(CA)CO; alternatively, the carbonyl spectra can be omitted and those assignments can be added to the bmrb file later). If one begins from a larger project and deletes other spectra, use the “dr” command to delete any unused assignments.  Also, try to avoid using “Q” in your assignment nomenclature in this subset of spectra.  Check the standard deviations in the resonance list for any unusually high values, to be sure there are no incorrect assignments.  This resonance list is then converted to a bmrb using the “sparkyRL2bmrb.pl” script as described above. Prior to moving on to structure determination programs, it is advisable to check the bmrb file for any missing or unusual shifts/typos using the AVS scripts, “missing_shifts.pl” and “validate_assignments.pl”. <br>		c.  Preparation of final bmrb file<br>For the most precise chemical shifts it is recommended that a final resonance list file (made by “rl”) be generated based on a subset of assigned spectra (2D NH-HSQC, 2D CH-HSQC aliphatic and aromatic, 3D HNCO and 3D HN(CA)CO; alternatively, the carbonyl spectra can be omitted and those assignments can be added to the bmrb file later). If one begins from a larger project and deletes other spectra, use the “dr” command to delete any unused assignments.  Also, try to avoid using “Q” in your assignment nomenclature in this subset of spectra.  Check the standard deviations in the resonance list for any unusually high values, to be sure there are no incorrect assignments.  This resonance list is then converted to a bmrb using the “sparkyRL2bmrb.pl” script as described above. Prior to moving on to structure determination programs, it is advisable to check the bmrb file for any missing or unusual shifts/typos using the AVS scripts, “missing_shifts.pl” and “validate_assignments.pl”. <br>

	== '''~~Citation~~''' ==		== '''Reference''' ==

	When using Sparky in your structure determination please cite:<br>    T.D. Goddard & D.G. Kneller, SPARKY 3,<br>    University of California, San Francisco<br>		When using Sparky in your structure determination please cite:<br>    T.D. Goddard & D.G. Kneller, SPARKY 3,<br>    University of California, San Francisco<br>

Jma at 18:28, 3 November 2009

2009-11-03T18:28:53Z

← Older revision		Revision as of 18:28, 3 November 2009
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	c.  Preparation of final bmrb file<br>For the most precise chemical shifts it is recommended that a final resonance list file (made by “rl”) be generated based on a subset of assigned spectra (2D NH-HSQC, 2D CH-HSQC aliphatic and aromatic, 3D HNCO and 3D HN(CA)CO; alternatively, the carbonyl spectra can be omitted and those assignments can be added to the bmrb file later). If one begins from a larger project and deletes other spectra, use the “dr” command to delete any unused assignments.  Also, try to avoid using “Q” in your assignment nomenclature in this subset of spectra.  Check the standard deviations in the resonance list for any unusually high values, to be sure there are no incorrect assignments.  This resonance list is then converted to a bmrb using the “sparkyRL2bmrb.pl” script as described above. Prior to moving on to structure determination programs, it is advisable to check the bmrb file for any missing or unusual shifts/typos using the AVS scripts, “missing_shifts.pl” and “validate_assignments.pl”. <br>		c.  Preparation of final bmrb file<br>For the most precise chemical shifts it is recommended that a final resonance list file (made by “rl”) be generated based on a subset of assigned spectra (2D NH-HSQC, 2D CH-HSQC aliphatic and aromatic, 3D HNCO and 3D HN(CA)CO; alternatively, the carbonyl spectra can be omitted and those assignments can be added to the bmrb file later). If one begins from a larger project and deletes other spectra, use the “dr” command to delete any unused assignments.  Also, try to avoid using “Q” in your assignment nomenclature in this subset of spectra.  Check the standard deviations in the resonance list for any unusually high values, to be sure there are no incorrect assignments.  This resonance list is then converted to a bmrb using the “sparkyRL2bmrb.pl” script as described above. Prior to moving on to structure determination programs, it is advisable to check the bmrb file for any missing or unusual shifts/typos using the AVS scripts, “missing_shifts.pl” and “validate_assignments.pl”. <br>

	== '''~~REFERENCES~~''' ==		== '''Citation''' ==

	When using Sparky in your structure determination please cite:<br>    T.D. Goddard & D.G. Kneller, SPARKY 3,<br>    University of California, San Francisco<br>		When using Sparky in your structure determination please cite:<br>    T.D. Goddard & D.G. Kneller, SPARKY 3,<br>    University of California, San Francisco<br>

Jma at 18:28, 3 November 2009

2009-11-03T18:28:29Z

← Older revision		Revision as of 18:28, 3 November 2009
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	== '''~~METHODS~~''' ==		== '''Methods''' ==

	==== Conversion of processed spectra to Sparky input format ====		==== Conversion of processed spectra to Sparky input format ====
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	ucsfdata –p1 –o output.ucsf input.ucsf		ucsfdata –p1 –o output.ucsf input.ucsf

	</pre>		</pre>

	==== Launching Sparky ====		==== Launching Sparky ====

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	===== Figure 1: Spectral views in Sparky =====		===== Figure 1: Spectral views in Sparky =====

	[[Image:Sparky fig1.png\|1200x800px]]		[[Image:Sparky fig1.png\|1200x800px]]

	==== Peak Picking<br> ====		==== Peak Picking<br> ====
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	===== Figure 2: Restricted peak pick box =====		===== Figure 2: Restricted peak pick box =====

	[[Image:Sparky kr.png]]		[[Image:Sparky kr.png]]

	==== Manipulating and Analyzing Multiple Spectra<br> ====		==== Manipulating and Analyzing Multiple Spectra<br> ====
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	===== Figure 3: Backbone spectra for a single spin system =====		===== Figure 3: Backbone spectra for a single spin system =====

	[[Image:Sparky BB.png\|1200x700px]]		[[Image:Sparky BB.png\|1200x700px]]

	==== Assignment and Peak Lists<br> ====		==== Assignment and Peak Lists<br> ====
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	The peaks2sparky.awk script can be obtained at:		The peaks2sparky.awk script can be obtained at:

	[http://www.nmr.chem.uu.nl/~eiso/help/index.html www.nmr.chem.uu.nl/~eiso/help/index.html] <br>		[http://www.nmr.chem.uu.nl/~eiso/help/index.html www.nmr.chem.uu.nl/~eiso/help/index.html] <br>

	==== Common Sparky Commands<br> ====		==== Common Sparky Commands<br> ====
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	a1, a2, a3:  add SW to peak in F1, F2, F3 dimension; for aliased spectra<br>A1, A2, A3:  subtract SW from peak in F1, F2, F3 dimension; for aliased spectra<br>at:  assignment tool; for assigning a peak<br>cl:  adjust colour of ornament<br>ct:  adjust contour levels and colours:<br>dr:  delete resonances not used in any peak assignment (cleans up resonance list)<br>eu:  undo last peak manipulation<br>it:  integration tool<br>kr:  restrictive peak picking tool<br>lt:  opens the peak list for a given spectrum; various options in here<br>oc:  ornament copy; for copying assignment/label information between spectra<br>ol:  overlay views; useful for comparing spectra<br>op: ornament paste<br>oz:  adjust size of ornament<br>pa:  select all peaks in a spectrum<br>pc:  peak center<br>pv:  list of sizes and peak counts in all open spectra<br>rl:   resonance list for the project; various functions and displays in there<br>rp:  read in a list of peaks in sparky format (i.e. from AutoAssign or PINE)<br>rr:  resonance rename<br>st:  spectrum tool; useful for global axes shift corrections<br>tb:  table of resonances for the project:  useful for seeing missing assignments<br>vc:  view centering; useful for going to a specific peak in a 3D selected in a 2D<br>vd:  view duplicate; duplicate view of a spectrum into another window<br>vR:  show assignments on edge of spectrum<br>vS:  show 1D slice on edge of spectrum<br>vt:  view settings; a variety of spectral settings including aspect ratio<br>xa:  show nucleus type on axis<br>xe:  special Python command for saving peak list in xeasy format<br>xr:  roll axes; useful for 3D and 4D spectra<br>xx:  axis transpose<br>yt:  synchronize axes of various spectra: useful for analyzing series of 3D’s<br>zf, zi, zo, zp:  zoom full spectrum, zoom in, zoom out, zoom previous<br><br>Commonly used pointer modes (for the mouse):<br>    F1: selection mode<br>    F6:  add a label<br>    F7:  add a line<br>    F8:  peak picking mode<br>    F10:  integration mode<br>    F11:  zoom mode		a1, a2, a3:  add SW to peak in F1, F2, F3 dimension; for aliased spectra<br>A1, A2, A3:  subtract SW from peak in F1, F2, F3 dimension; for aliased spectra<br>at:  assignment tool; for assigning a peak<br>cl:  adjust colour of ornament<br>ct:  adjust contour levels and colours:<br>dr:  delete resonances not used in any peak assignment (cleans up resonance list)<br>eu:  undo last peak manipulation<br>it:  integration tool<br>kr:  restrictive peak picking tool<br>lt:  opens the peak list for a given spectrum; various options in here<br>oc:  ornament copy; for copying assignment/label information between spectra<br>ol:  overlay views; useful for comparing spectra<br>op: ornament paste<br>oz:  adjust size of ornament<br>pa:  select all peaks in a spectrum<br>pc:  peak center<br>pv:  list of sizes and peak counts in all open spectra<br>rl:   resonance list for the project; various functions and displays in there<br>rp:  read in a list of peaks in sparky format (i.e. from AutoAssign or PINE)<br>rr:  resonance rename<br>st:  spectrum tool; useful for global axes shift corrections<br>tb:  table of resonances for the project:  useful for seeing missing assignments<br>vc:  view centering; useful for going to a specific peak in a 3D selected in a 2D<br>vd:  view duplicate; duplicate view of a spectrum into another window<br>vR:  show assignments on edge of spectrum<br>vS:  show 1D slice on edge of spectrum<br>vt:  view settings; a variety of spectral settings including aspect ratio<br>xa:  show nucleus type on axis<br>xe:  special Python command for saving peak list in xeasy format<br>xr:  roll axes; useful for 3D and 4D spectra<br>xx:  axis transpose<br>yt:  synchronize axes of various spectra: useful for analyzing series of 3D’s<br>zf, zi, zo, zp:  zoom full spectrum, zoom in, zoom out, zoom previous<br><br>Commonly used pointer modes (for the mouse):<br>    F1: selection mode<br>    F6:  add a label<br>    F7:  add a line<br>    F8:  peak picking mode<br>    F10:  integration mode<br>    F11:  zoom mode

	<br>		<br>

	==== Example Protein Assignment Project<br> ====		==== Example Protein Assignment Project<br> ====

Jma at 18:28, 3 November 2009

2009-11-03T18:28:09Z

← Older revision		Revision as of 18:28, 3 November 2009
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	= '''Sparky''' =		= '''Sparky''' =

	== '''~~INTRODUCTION~~''' ==		== '''Introduction''' ==

	Sparky is a software package developed at the University of San Francisco for visualizing and analyzing multidimensional (2D, 3D or 4D) NMR spectra.  Sparky plays a critical role as the link between spectral data and assignment/structure determination programs.  The input for the program is processed spectra from various formats (NMRPipe, Felix, Varian or Bruker) converted into Sparky (i.e., “ucsf” format) via processing scripts supplied with the program.  One can output a variety of data from Sparky including:  chemical shift assignments, peak lists, and post script images of spectra.   In the following sections we describe the practical aspects of using Sparky and standard approaches employed by NESG researchers using this program in structure determination projects.  A descriptive on-line manual for a recent Sparky version (3.115) is available at: [http://www.cgl.ucsf.edu/home/sparky/manual/index.html www.cgl.ucsf.edu/home/sparky/manual/index.html].		Sparky is a software package developed at the University of San Francisco for visualizing and analyzing multidimensional (2D, 3D or 4D) NMR spectra.  Sparky plays a critical role as the link between spectral data and assignment/structure determination programs.  The input for the program is processed spectra from various formats (NMRPipe, Felix, Varian or Bruker) converted into Sparky (i.e., “ucsf” format) via processing scripts supplied with the program.  One can output a variety of data from Sparky including:  chemical shift assignments, peak lists, and post script images of spectra.   In the following sections we describe the practical aspects of using Sparky and standard approaches employed by NESG researchers using this program in structure determination projects.  A descriptive on-line manual for a recent Sparky version (3.115) is available at: [http://www.cgl.ucsf.edu/home/sparky/manual/index.html www.cgl.ucsf.edu/home/sparky/manual/index.html].



	== '''METHODS''' ==		== '''METHODS''' ==

Jma: moved NESG:Sparky to Sparky

2009-11-01T06:13:03Z

moved NESG:Sparky to Sparky

← Older revision	Revision as of 06:13, 1 November 2009
(No difference)

Jma at 18:33, 31 October 2009

2009-10-31T18:33:32Z

← Older revision		Revision as of 18:33, 31 October 2009
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	<br>		<br>

	==== ~~7. ~~ Example Protein Assignment Project<br> ====		==== Example Protein Assignment Project<br> ====

	a.  Backbone assignments<br>When starting an assignment project on a specific protein it is recommended that all Sparky files are collected in a specific project directory.  In a conventional triple resonance backbone assignment one matches intraresidue and sequential C’, Cα, and Cβ resonances in 2D NH-HSQC and 3D HNCO, HN(CA)CO, CBCA(CO)NH, and HNCACB, for example (Figure 3, above).  For automated backbone assignment using programs such as AutoAssign or the PINE server (http://miranda.nmrfam.wisc.edu/PINE/) it is important that the peak lists are properly registered to each other, particularly in the N and HN dimensions.  Any systematic shifting between spectra can be corrected using the “st” command.  Peak lists should contain chemical shift information in each dimension and the peak intensities.  For input into AutoAssign, additional spin system information can be specified in the Notes column; in the case of PINE, one should remove this column.  Assigned peak lists in Sparky format from either AutoAssign or PINE can be read back into the spectra using the “rp” command.  One can then check the assignments for each NH spin system using the “vc” command, using the NH-HSQC as the root spectrum.  One can also fill in the Hα and Hβ assignments in the HBHA(CO)NH spectrum.  At this stage one can make a preliminary bmrb file (using the “rl” and “sparkyRL2bmrb.pl” script), and use this to make a CH-HSQC list containing predicted resonance assignments using the “bmrbACS2SparkyPks.pl” script as follows:		a.  Backbone assignments<br>When starting an assignment project on a specific protein it is recommended that all Sparky files are collected in a specific project directory.  In a conventional triple resonance backbone assignment one matches intraresidue and sequential C’, Cα, and Cβ resonances in 2D NH-HSQC and 3D HNCO, HN(CA)CO, CBCA(CO)NH, and HNCACB, for example (Figure 3, above).  For automated backbone assignment using programs such as AutoAssign or the PINE server (http://miranda.nmrfam.wisc.edu/PINE/) it is important that the peak lists are properly registered to each other, particularly in the N and HN dimensions.  Any systematic shifting between spectra can be corrected using the “st” command.  Peak lists should contain chemical shift information in each dimension and the peak intensities.  For input into AutoAssign, additional spin system information can be specified in the Notes column; in the case of PINE, one should remove this column.  Assigned peak lists in Sparky format from either AutoAssign or PINE can be read back into the spectra using the “rp” command.  One can then check the assignments for each NH spin system using the “vc” command, using the NH-HSQC as the root spectrum.  One can also fill in the Hα and Hβ assignments in the HBHA(CO)NH spectrum.  At this stage one can make a preliminary bmrb file (using the “rl” and “sparkyRL2bmrb.pl” script), and use this to make a CH-HSQC list containing predicted resonance assignments using the “bmrbACS2SparkyPks.pl” script as follows:

Jma at 18:31, 31 October 2009

2009-10-31T18:31:25Z

← Older revision		Revision as of 18:31, 31 October 2009
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	[http://www.nmr.chem.uu.nl/~eiso/help/index.html www.nmr.chem.uu.nl/~eiso/help/index.html] <br>		[http://www.nmr.chem.uu.nl/~eiso/help/index.html www.nmr.chem.uu.nl/~eiso/help/index.html] <br>

	==== ~~6. ~~ Common Sparky Commands<br> ====		==== Common Sparky Commands<br> ====

	There are numerous useful two-letter commands that can speed up spectral analysis in Sparky.  Here is a list of commonly used accelerators:		There are numerous useful two-letter commands that can speed up spectral analysis in Sparky.  Here is a list of commonly used accelerators:
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	a1, a2, a3:  add SW to peak in F1, F2, F3 dimension; for aliased spectra<br>A1, A2, A3:  subtract SW from peak in F1, F2, F3 dimension; for aliased spectra<br>at:  assignment tool; for assigning a peak<br>cl:  adjust colour of ornament<br>ct:  adjust contour levels and colours:<br>dr:  delete resonances not used in any peak assignment (cleans up resonance list)<br>eu:  undo last peak manipulation<br>it:  integration tool<br>kr:  restrictive peak picking tool<br>lt:  opens the peak list for a given spectrum; various options in here<br>oc:  ornament copy; for copying assignment/label information between spectra<br>ol:  overlay views; useful for comparing spectra<br>op: ornament paste<br>oz:  adjust size of ornament<br>pa:  select all peaks in a spectrum<br>pc:  peak center<br>pv:  list of sizes and peak counts in all open spectra<br>rl:   resonance list for the project; various functions and displays in there<br>rp:  read in a list of peaks in sparky format (i.e. from AutoAssign or PINE)<br>rr:  resonance rename<br>st:  spectrum tool; useful for global axes shift corrections<br>tb:  table of resonances for the project:  useful for seeing missing assignments<br>vc:  view centering; useful for going to a specific peak in a 3D selected in a 2D<br>vd:  view duplicate; duplicate view of a spectrum into another window<br>vR:  show assignments on edge of spectrum<br>vS:  show 1D slice on edge of spectrum<br>vt:  view settings; a variety of spectral settings including aspect ratio<br>xa:  show nucleus type on axis<br>xe:  special Python command for saving peak list in xeasy format<br>xr:  roll axes; useful for 3D and 4D spectra<br>xx:  axis transpose<br>yt:  synchronize axes of various spectra: useful for analyzing series of 3D’s<br>zf, zi, zo, zp:  zoom full spectrum, zoom in, zoom out, zoom previous<br><br>Commonly used pointer modes (for the mouse):<br>    F1: selection mode<br>    F6:  add a label<br>    F7:  add a line<br>    F8:  peak picking mode<br>    F10:  integration mode<br>    F11:  zoom mode		a1, a2, a3:  add SW to peak in F1, F2, F3 dimension; for aliased spectra<br>A1, A2, A3:  subtract SW from peak in F1, F2, F3 dimension; for aliased spectra<br>at:  assignment tool; for assigning a peak<br>cl:  adjust colour of ornament<br>ct:  adjust contour levels and colours:<br>dr:  delete resonances not used in any peak assignment (cleans up resonance list)<br>eu:  undo last peak manipulation<br>it:  integration tool<br>kr:  restrictive peak picking tool<br>lt:  opens the peak list for a given spectrum; various options in here<br>oc:  ornament copy; for copying assignment/label information between spectra<br>ol:  overlay views; useful for comparing spectra<br>op: ornament paste<br>oz:  adjust size of ornament<br>pa:  select all peaks in a spectrum<br>pc:  peak center<br>pv:  list of sizes and peak counts in all open spectra<br>rl:   resonance list for the project; various functions and displays in there<br>rp:  read in a list of peaks in sparky format (i.e. from AutoAssign or PINE)<br>rr:  resonance rename<br>st:  spectrum tool; useful for global axes shift corrections<br>tb:  table of resonances for the project:  useful for seeing missing assignments<br>vc:  view centering; useful for going to a specific peak in a 3D selected in a 2D<br>vd:  view duplicate; duplicate view of a spectrum into another window<br>vR:  show assignments on edge of spectrum<br>vS:  show 1D slice on edge of spectrum<br>vt:  view settings; a variety of spectral settings including aspect ratio<br>xa:  show nucleus type on axis<br>xe:  special Python command for saving peak list in xeasy format<br>xr:  roll axes; useful for 3D and 4D spectra<br>xx:  axis transpose<br>yt:  synchronize axes of various spectra: useful for analyzing series of 3D’s<br>zf, zi, zo, zp:  zoom full spectrum, zoom in, zoom out, zoom previous<br><br>Commonly used pointer modes (for the mouse):<br>    F1: selection mode<br>    F6:  add a label<br>    F7:  add a line<br>    F8:  peak picking mode<br>    F10:  integration mode<br>    F11:  zoom mode

	<br>		<br>

	==== 7.  Example Protein Assignment Project<br> ====		==== 7.  Example Protein Assignment Project<br> ====