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2002 NANUC Training Course2002 NANUC Training Course

NMRVIEW for BeginnersNMRVIEW for Beginners

Friday Oct. 11Friday Oct. 11th,th, 8am 8am

Ryan McKayRyan McKay

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OutlineOutline• InstallationInstallation

– Most common problem(s)Most common problem(s)

• Starting upStarting up– Built in tools and help filesBuilt in tools and help files

• DataData– nmrPipe examplenmrPipe example

• WindowsWindows• SpectraSpectra• ReferencingReferencing• Cross-hairsCross-hairs• Picking PeaksPicking Peaks• AssignmentsAssignments• Strip plotsStrip plots

– 40 slides at 3-4 min/slide 40 slides at 3-4 min/slide

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Installation and trouble shooting.Installation and trouble shooting.• Platforms available:Platforms available:

– Runs on Sun, SGI, Linux, Mac OSXRuns on Sun, SGI, Linux, Mac OSX– Remote display to all types via Xwindows.Remote display to all types via Xwindows.

• NANUC additions set up for OSXNANUC additions set up for OSX– Downloadable package (include in CD)Downloadable package (include in CD)– Automatic installation = No user set up requiredAutomatic installation = No user set up required– Documentation (included in CD)Documentation (included in CD)

• NMRVIEW installation instructionsNMRVIEW installation instructions– http://www.nmrview.com/manual/README.htmlhttp://www.nmrview.com/manual/README.html

• Need the program files, put in a directory that the Need the program files, put in a directory that the computer looks for programs (computer looks for programs (e.g.e.g. /usr/local/bin/usr/local/bin or or /usr/local/usr/local))

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Trouble shooting - Environment pathTrouble shooting - Environment path

• If the program is already installed but not working check: If the program is already installed but not working check: which nmrviewwhich nmrview

• if the program is not found you’ve got to tell the computer where it isif the program is not found you’ve got to tell the computer where it is

• Find program and update “path”Find program and update “path”– .cshrc set up.cshrc set up

echo $pathecho $path

set path = ($path /Users/ryan/bin)set path = ($path /Users/ryan/bin)

– nmrview requires computer resources and additional tools (e.g. tcl and tkl)nmrview requires computer resources and additional tools (e.g. tcl and tkl)

– Make additions to your .cshrc file or ….Make additions to your .cshrc file or ….

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Starting up (Install cont.)Starting up (Install cont.)

• Different versions of tcl and tklDifferent versions of tcl and tkl• Programs may require a particular version of tcl and tklPrograms may require a particular version of tcl and tkl

• To avoid problems, only load the particular type you want as needed for the To avoid problems, only load the particular type you want as needed for the program you’re runningprogram you’re running

more ~ryan/bin/nmrviewmore ~ryan/bin/nmrview

– The last line shows an example of how you can get additional scripts, The last line shows an example of how you can get additional scripts, programs, or preferences loaded into nmrview at startup.programs, or preferences loaded into nmrview at startup.

– Here we show how Pascal’s Here we show how Pascal’s nanuc_tcl navigatornanuc_tcl navigator gets loaded gets loaded automatically.automatically.

#!/bin/cshsetenv NMRVIEW5HOME /usr/local/nmrview5setenv TCL_LIBRARY ${NMRVIEW5HOME}/tcl8.3setenv TK_LIBRARY ${NMRVIEW5HOME}/tcl8.3${NMRVIEW5HOME}/nmrview5.0.15.XDarwin -- -s ${NMRVIEW5HOME}/nanuc_tcl/startfile

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NMRVIEW - NANUC Start fileNMRVIEW - NANUC Start file[Esposito:~/bin] ryan: more /usr/local/nmrview5/nanuc_tcl/startfileoption add *Font {Helvetica -12}source /usr/local/nmrview5/nanuc_tcl/dkffont.tclsource /usr/local/nmrview5/nanuc_tcl/FontSelection.tclsource /usr/local/nmrview5/nanuc_tcl/closestpeak.tclsource /usr/local/nmrview5/nanuc_tcl/fillshifts.tclsource /usr/local/nmrview5/nanuc_tcl/jextracthnha.tclsource /usr/local/nmrview5/nanuc_tcl/peakanal.tclsource /usr/local/nmrview5/nanuc_tcl/peakid.tclsource /usr/local/nmrview5/nanuc_tcl/searchpeaks.tclsource /usr/local/nmrview5/nanuc_tcl/symmetry.tclsource /usr/local/nmrview5/nanuc_tcl/relaxv3.2.tclsource /usr/local/nmrview5/nanuc_tcl/keys.tclsource /usr/local/nmrview5/nanuc_tcl/navig_v4.5.tclsource /usr/local/nmrview5/nanuc_tcl/noe-curt-fix-aria-aalim.tclsource /usr/local/nmrview5/nanuc_tcl/extractC13restraints.tclsource /usr/local/nmrview5/nanuc_tcl/extract-psi.tcl

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Startup SummaryStartup Summary

• Program and files need to be installedProgram and files need to be installed• Your environment/login needs to know where to find Your environment/login needs to know where to find

the program once it’s therethe program once it’s there• Either tell the computer each time you login, or set up Either tell the computer each time you login, or set up

files to do this for you automatically: when you start the files to do this for you automatically: when you start the program or upon login.program or upon login.

• 95% of the problems are environment associated95% of the problems are environment associated• Customization - either through startup scripts or Customization - either through startup scripts or

environmental variablesenvironmental variables

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NMRVIEW - built in tools NMRVIEW - built in tools

• How do find out more about a tool?How do find out more about a tool?– E.g.E.g. HNHA HNHA

/usr/local/nmrview5/nvtclExt/hnha.tcl/usr/local/nmrview5/nvtclExt/hnha.tcl

# hnha.tcl# Analyzes an HNHA peaklist# and produces a list of J-values and angle constraints.

# The coupling constant is calculated as described# in Kuboniwa et al. J. Biomol. NMR 4 (1994), 871-878:## IX/ID = -tan2(2*pi*[epsilon]*[JHNHA])## where IX is the cross-peak intensity, ID is# the diagonal peak intensity, epsilon is the HNHA# de/rephasing period.

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HELP !!! HELP !!! filesfiles

• Website manual for NMRVIEWWebsite manual for NMRVIEW– http://www.nmrview.com/manual/index.htmlhttp://www.nmrview.com/manual/index.html

• README file installed with programREADME file installed with program• Internal “help” programInternal “help” program

– External viewerExternal viewer– cd /usr/local/nmrview5/help/cd /usr/local/nmrview5/help/

• NMRVIEW mailing listNMRVIEW mailing list• http://www.nmrview.com/archive/maillist.htmlhttp://www.nmrview.com/archive/maillist.html

• Reformatted manualReformatted manual• Step-by-Step tutorial for new users?Step-by-Step tutorial for new users?

– 10 a.a. fully labeled peptide with instructions10 a.a. fully labeled peptide with instructions

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NMRPIPE Data exampleNMRPIPE Data example

• We import data from NMRPipeWe import data from NMRPipepipe2view.compipe2view.com

• 2003 NANUC NMRPipe training course2003 NANUC NMRPipe training course• It is possible to import data directly in to the nmrview It is possible to import data directly in to the nmrview

program.program.

#! /bin/cshxyz2pipe -in 3d_data/hnco%03d.ft3 -x -verb \| pipe2xyz -nv -out hnco.nv

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Opening ViewOpening View

Terminal Window

nmrviewcommand linewindow

Main Pull DownMenus

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Windows - Can you ever have enough?Windows - Can you ever have enough?

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Realistic NMRViewRealistic NMRView

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MenusMenus• The overlying theme of NMRVIEW:The overlying theme of NMRVIEW:

• ““You can never have too many windows”You can never have too many windows”

• Everything brings up its own window.Everything brings up its own window.

• The majority of what you’re looking for is in the pull down menusThe majority of what you’re looking for is in the pull down menus

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SpectraSpectra• How to load a spectra for viewing?How to load a spectra for viewing?

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Getting data for display in a windowGetting data for display in a window

• Data must be loaded, and then assigned for display in a Data must be loaded, and then assigned for display in a particular window.particular window.

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Putting the window and data togetherPutting the window and data together

1.) Right click in the window

2.) Select attributes

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Attributes (cont.)Attributes (cont.)

• Note: Colors, and X Y Z and 1 2 3 pull down menusNote: Colors, and X Y Z and 1 2 3 pull down menus

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Cross-hairs and mouse buttonsCross-hairs and mouse buttons• Left mouse button = blackLeft mouse button = black Middle=redMiddle=red• Right mouse = menusRight mouse = menus

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Multiple Spectra with same cursorMultiple Spectra with same cursor

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Getting Rid of a MenuGetting Rid of a Menu

-Right-Click

-Now what?

-1.) tear off

-2.) Attributes then close

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ReferencingReferencing

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Referencing (cont.)Referencing (cont.)

Ref-Correct assignment

Lvl-Time saver

Writing or Reading-Directory location

Labels

-Cursor control

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Read Sequence FileRead Sequence File

• Sequence fileSequence file metileglyvallysgluleuargaspalapheargglu

Seq. File

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Assigning Chemical ShiftsAssigning Chemical Shifts

• After the sequence file is read in you After the sequence file is read in you can start an assignment table.can start an assignment table.

• *Common problem**Common problem*– Program directoryProgram directory

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Making a New Peak TableMaking a New Peak Table• Assign Pull DownAssign Pull Down

– PeaksPeaks

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Automatic Picking of PeaksAutomatic Picking of Peaks

** peaks are not saved until you give the instruction**

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Displaying PeaksDisplaying Peaks• Showing peaks you’ve already pickedShowing peaks you’ve already picked

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Peak Attributes PanelPeak Attributes Panel

• Like the Like the Display AttributesDisplay Attributes, which ever spectra is , which ever spectra is “active” is the one this Peak Attributes controls.“active” is the one this Peak Attributes controls.– Peak ListPeak List

– ColorColor

– Plane offPlane off

– LabelLabel

– Peak TypePeak Type

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Assigning Peaks SummaryAssigning Peaks Summary

• Automatic picking of peaks appearing in the spectraAutomatic picking of peaks appearing in the spectra– Selection box or entire window, or entire 3DSelection box or entire window, or entire 3D

– Filtering of diagonal or solventFiltering of diagonal or solvent

• Identification by the user of spin-systems and Identification by the user of spin-systems and sequential connectivity (sequential connectivity (e.g.e.g. SmartNoteBook). SmartNoteBook).– Identification of intra- and inter-residue cross-peaks.Identification of intra- and inter-residue cross-peaks.

• Assignment of chemical shifts to specific atoms (see Assignment of chemical shifts to specific atoms (see “reading sequence file”) and filling in of the “reading sequence file”) and filling in of the assignPanel (see below) window.assignPanel (see below) window.

• Using “patterns” for the “identification” process (next)Using “patterns” for the “identification” process (next)

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PatternsPatterns

• Getting the computer to recognize peaks based on the Getting the computer to recognize peaks based on the chemical shiftchemical shift– assignPanel must have the correct chemical shifts entered and assignPanel must have the correct chemical shifts entered and

“Update” (see Assigning Chemical Shifts)“Update” (see Assigning Chemical Shifts)

– Tolerance for the search must be set (see Referencing)Tolerance for the search must be set (see Referencing)

– NMRView must be told how to correlate the chemical shifts NMRView must be told how to correlate the chemical shifts of the peaks with the ones in the assignPanelof the peaks with the ones in the assignPanel

– ““Pattern” lets the program know what axis on the spectra Pattern” lets the program know what axis on the spectra corresponds to what type of atom and where to look for it.corresponds to what type of atom and where to look for it.

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Patterns for Assigning PeaksPatterns for Assigning Peaks

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Patterns (examples)Patterns (examples)• 1515N-NOESY, N-NOESY, 1313C-NOESY, HCCH-TOCSYC-NOESY, HCCH-TOCSY

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Patterns (examples summary)Patterns (examples summary)15N-NOESY

HCCH-TOCSY13C-NOESY

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Identify WindowIdentify Window• Opening the “peakId” windowOpening the “peakId” window

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peakId Noesy ExamplepeakId Noesy Example

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Moving the viewMoving the view• PIPP Short cut keysPIPP Short cut keys

– Keys mapped to Keys mapped to particular functionsparticular functions

• d = drawd = draw• e = expand (expand e = expand (expand

region between region between cross-hairs)cross-hairs)

• + = zoom out+ = zoom out• - = zoom in- = zoom in• 4 8 6 2 = up down 4 8 6 2 = up down

left right, move view left right, move view regionregion

• 5 = center on black 5 = center on black cursorcursor

e.g.e.g. /usr/local/nmrview5/nanuc_tcl/keys.tcl /usr/local/nmrview5/nanuc_tcl/keys.tcl

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Moving the view (cont.)Moving the view (cont.)

• Additional Short cutsAdditional Short cuts• Up and down arrows = move up and down in 3D planesUp and down arrows = move up and down in 3D planes

• Sun platform - Sun platform - altalt key in combination may be required key in combination may be required

• p = previous viewp = previous view

• Pascal’s specific keysPascal’s specific keys• t = Find Symmetrical Peakt = Find Symmetrical Peak

• c = find closest picked peak (doesn’t have to be assigned)c = find closest picked peak (doesn’t have to be assigned)

• z = on an hsqc, zoom all 3D spectra to that HN,N positionz = on an hsqc, zoom all 3D spectra to that HN,N position

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Strip plotsStrip plots

• Used to present data side-by-side very efficiently and to Used to present data side-by-side very efficiently and to allow faster confirmation of sequential assignmentsallow faster confirmation of sequential assignments– Need to use a new nameNeed to use a new name

– Can’t use capitols in the nameCan’t use capitols in the name

– No spacesNo spaces

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Strip Plot WindowStrip Plot Window

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Strip Plot Window (cont.)Strip Plot Window (cont.)

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Summary of the BasicsSummary of the Basics

• Set up and help filesSet up and help files

• Common troubles at start upCommon troubles at start up

• How to load dataHow to load data

• WindowsWindows

• MenusMenus

• Cross-hairsCross-hairs

• PeaksPeaks

• AssignmentsAssignments

• Moving aroundMoving around

• Strip plotsStrip plots