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2002 NANUC Training Course

2002 NANUC Training Course. NMRVIEW for Beginners Friday Oct. 11 th, 8am Ryan McKay. Outline. Installation Most common problem(s) Starting up Built in tools and help files Data nmrPipe example Windows Spectra Referencing Cross-hairs Picking Peaks Assignments Strip plots

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2002 NANUC Training Course

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  1. 2002 NANUC Training Course NMRVIEW for Beginners Friday Oct. 11th, 8am Ryan McKay 1

  2. Outline • Installation • Most common problem(s) • Starting up • Built in tools and help files • Data • nmrPipe example • Windows • Spectra • Referencing • Cross-hairs • Picking Peaks • Assignments • Strip plots • 40 slides at 3-4 min/slide 2

  3. Installation and trouble shooting. • Platforms available: • Runs on Sun, SGI, Linux, Mac OSX • Remote display to all types via Xwindows. • NANUC additions set up for OSX • Downloadable package (include in CD) • Automatic installation = No user set up required • Documentation (included in CD) • NMRVIEW installation instructions • http://www.nmrview.com/manual/README.html • Need the program files, put in a directory that the computer looks for programs (e.g./usr/local/bin or /usr/local) 3

  4. Trouble shooting - Environment path • If the program is already installed but not working check: which nmrview • if the program is not found you’ve got to tell the computer where it is • Find program and update “path” • .cshrc set up echo $path set path = ($path /Users/ryan/bin) • nmrview requires computer resources and additional tools (e.g. tcl and tkl) • Make additions to your .cshrc file or …. 4

  5. Starting up (Install cont.) • Different versions of tcl and tkl • Programs may require a particular version of tcl and tkl • To avoid problems, only load the particular type you want as needed for the program you’re running more ~ryan/bin/nmrview • The last line shows an example of how you can get additional scripts, programs, or preferences loaded into nmrview at startup. • Here we show how Pascal’s nanuc_tcl navigator gets loaded automatically. #!/bin/csh setenv NMRVIEW5HOME /usr/local/nmrview5 setenv TCL_LIBRARY ${NMRVIEW5HOME}/tcl8.3 setenv TK_LIBRARY ${NMRVIEW5HOME}/tcl8.3 ${NMRVIEW5HOME}/nmrview5.0.15.XDarwin -- -s ${NMRVIEW5HOME}/nanuc_tcl/startfile 5

  6. NMRVIEW - NANUC Start file [Esposito:~/bin] ryan: more /usr/local/nmrview5/nanuc_tcl/startfile option add *Font {Helvetica -12} source /usr/local/nmrview5/nanuc_tcl/dkffont.tcl source /usr/local/nmrview5/nanuc_tcl/FontSelection.tcl source /usr/local/nmrview5/nanuc_tcl/closestpeak.tcl source /usr/local/nmrview5/nanuc_tcl/fillshifts.tcl source /usr/local/nmrview5/nanuc_tcl/jextracthnha.tcl source /usr/local/nmrview5/nanuc_tcl/peakanal.tcl source /usr/local/nmrview5/nanuc_tcl/peakid.tcl source /usr/local/nmrview5/nanuc_tcl/searchpeaks.tcl source /usr/local/nmrview5/nanuc_tcl/symmetry.tcl source /usr/local/nmrview5/nanuc_tcl/relaxv3.2.tcl source /usr/local/nmrview5/nanuc_tcl/keys.tcl source /usr/local/nmrview5/nanuc_tcl/navig_v4.5.tcl source /usr/local/nmrview5/nanuc_tcl/noe-curt-fix-aria-aalim.tcl source /usr/local/nmrview5/nanuc_tcl/extractC13restraints.tcl source /usr/local/nmrview5/nanuc_tcl/extract-psi.tcl 6

  7. Startup Summary • Program and files need to be installed • Your environment/login needs to know where to find the program once it’s there • Either tell the computer each time you login, or set up files to do this for you automatically: when you start the program or upon login. • 95% of the problems are environment associated • Customization - either through startup scripts or environmental variables 7

  8. NMRVIEW - built in tools • How do find out more about a tool? • E.g. HNHA /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. 8

  9. HELP !!! files • Website manual for NMRVIEW • http://www.nmrview.com/manual/index.html • README file installed with program • Internal “help” program • External viewer • cd /usr/local/nmrview5/help/ • NMRVIEW mailing list • http://www.nmrview.com/archive/maillist.html • Reformatted manual • Step-by-Step tutorial for new users? • 10 a.a. fully labeled peptide with instructions 9

  10. NMRPIPE Data example • We import data from NMRPipe pipe2view.com • 2003 NANUC NMRPipe training course • It is possible to import data directly in to the nmrview program. #! /bin/csh xyz2pipe -in 3d_data/hnco%03d.ft3 -x -verb \ | pipe2xyz -nv -out hnco.nv 10

  11. Opening View Terminal Window Main Pull Down Menus nmrview command line window 11

  12. Windows - Can you ever have enough? 12

  13. Realistic NMRView 13

  14. Menus • The overlying theme of NMRVIEW: • “You can never have too many windows” • Everything brings up its own window. • The majority of what you’re looking for is in the pull down menus 14

  15. Spectra • How to load a spectra for viewing? 15

  16. Getting data for display in a window • Data must be loaded, and then assigned for display in a particular window. 16

  17. Putting the window and data together 2.) Select attributes 1.) Right click in the window 17

  18. Attributes (cont.) • Note: Colors, and X Y Z and 1 2 3 pull down menus 18

  19. Cross-hairs and mouse buttons • Left mouse button = black Middle=red • Right mouse = menus 19

  20. Multiple Spectra with same cursor 20

  21. Getting Rid of a Menu • Right-Click • Now what? • 1.) tear off • 2.) Attributes then close 21

  22. Referencing 22

  23. Referencing (cont.) Labels -Cursor control Ref -Correct assignment Lvl -Time saver Writing or Reading -Directory location 23

  24. Read Sequence File Seq. File • Sequence file met ile gly val lys glu leu arg asp ala phe arg glu 24

  25. Assigning Chemical Shifts • After the sequence file is read in you can start an assignment table. • *Common problem* • Program directory 25

  26. Making a New Peak Table • Assign Pull Down • Peaks 26

  27. Automatic Picking of Peaks ** peaks are not saved until you give the instruction** 27

  28. Displaying Peaks • Showing peaks you’ve already picked 28

  29. Peak Attributes Panel • Like the Display Attributes, which ever spectra is “active” is the one this Peak Attributes controls. • Peak List • Color • Plane off • Label • Peak Type 29

  30. Assigning Peaks Summary • Automatic picking of peaks appearing in the spectra • Selection box or entire window, or entire 3D • Filtering of diagonal or solvent • Identification by the user of spin-systems and sequential connectivity (e.g. SmartNoteBook). • Identification of intra- and inter-residue cross-peaks. • Assignment of chemical shifts to specific atoms (see “reading sequence file”) and filling in of the assignPanel (see below) window. • Using “patterns” for the “identification” process (next) 30

  31. Patterns • Getting the computer to recognize peaks based on the chemical shift • assignPanel must have the correct chemical shifts entered and “Update” (see Assigning Chemical Shifts) • Tolerance for the search must be set (see Referencing) • NMRView must be told how to correlate the chemical shifts of the peaks with the ones in the assignPanel • “Pattern” lets the program know what axis on the spectra corresponds to what type of atom and where to look for it. 31

  32. Patterns for Assigning Peaks 32

  33. Patterns (examples) • 15N-NOESY, 13C-NOESY, HCCH-TOCSY 33

  34. Patterns (examples summary) 15N-NOESY 13C-NOESY HCCH-TOCSY 34

  35. Identify Window • Opening the “peakId” window 35

  36. peakId Noesy Example 36

  37. Moving the view • e.g. /usr/local/nmrview5/nanuc_tcl/keys.tcl • PIPP Short cut keys • Keys mapped to particular functions • d = draw • e = expand (expand region between cross-hairs) • + = zoom out • - = zoom in • 4 8 6 2 = up down left right, move view region • 5 = center on black cursor 37

  38. Moving the view (cont.) • Additional Short cuts • Up and down arrows = move up and down in 3D planes • Sun platform - alt key in combination may be required • p = previous view • Pascal’s specific keys • t = Find Symmetrical Peak • c = find closest picked peak (doesn’t have to be assigned) • z = on an hsqc, zoom all 3D spectra to that HN,N position 38

  39. Strip plots • Used to present data side-by-side very efficiently and to allow faster confirmation of sequential assignments • Need to use a new name • Can’t use capitols in the name • No spaces 39

  40. Strip Plot Window 40

  41. Strip Plot Window (cont.) 41

  42. Summary of the Basics • Set up and help files • Common troubles at start up • How to load data • Windows • Menus • Cross-hairs • Peaks • Assignments • Moving around • Strip plots 42

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