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Magnet_BodyHFNMRC : High Field NMR Center


NMR Related Software

NMR data processing software

  • XWINNMR  (process NMR data) :
    1. Purpose:
      XWINNMR is the software developped by Bruker to monitor their spectrometer (acquire, process and analyse NMR data). Xwinnmr provides data processing and analysis routines which can be performed manually or in automation. Particular attention has been paid to the ease and efficiency of multidimensional data analysis, including phasing, real-time adjustment of contour levels or planers, and presentation of expanded regions. XWIN-NMR can import data formats from various program packages.
    2. Using XWINNMR
        STEP :
      1. prepare data sets
        acquisition data (Xwinnmr)
        fid  -->   the binary data of 1D
        (Directory : /<diskname>/data/<username>/nmr /filename/<exp#>/fid)
        ser  -->   the binary data of 2D and 3D
        (Directory : /<diskname>/data/<username>/nmr /filename/<exp#>/ser)
      2. data processing
        Xwinnmr  -->  start the porgram
        [file]  -->   read the acquisition data
        edp  -->  edit process parameter
        ft(1D)  -->  Fourier transfer for 1D (xfb for 2D and 3D)
        [phase]  -->  adjust the phase angle

    ( refer to http://www.bruker.de/analytic/nmr-dep/nmrsoftw/prodinfo/nmr_suit/xwin-nmr/index.htm )
     
  • nmrPipe   (process NMR data) :
    1. Purpose:
      NMRPipe provides comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. Conversion facilities specifically for Varian and Bruker binary time-domain data are provided, as well as general purpose facilities accommodating most other formats. All data is converted to a common format with a uniform organization of real and imaginary points.
    2. Using nmrPipe
        STEP :
      1. prepare data sets
        acquisition data
        ser  -->   the binary data of 2D and 3D
        (Directory : /<diskname>/data/<username>/nmr /filename/<expt #>/ser)
      2. data conversion
        Bruker or varian  -->   Edit conversion script and execute script to generate a *.fid file
      3. data processing
        nmrpipe
        > processing script  -->   processing schemes must edit it to specify the input and output files, and phasing parameters. Finally generate *.ft (2D) and *xyz%3d.ft (3D) files

    ( refer to http://hhmi.umbc.edu/toolkit/processing/nih/NMRPipe.html )
     

NMR data analysis software

  • AURELIA  (analyze NMR data) :
    1. Purpose:
      AURELIA supports the semi-auto XWINNMRmated analysis of all types of 2D, 3D and 4D spectra. A rich collection of algorithms (e.g., for multiplet analysis, spin system search, volume/distance calculation, NOESY backcalculation and spectra enhancements) together with many optimized display tools help you to save a lot of time.
    2. Using Aurelia
        STEP :
      1. prepare data sets
        XWINNMR processed data format files include
        2rr  -->   the binary data of 2D
        (Directory : /<diskname>/data/<username>/nmr /filename/<expt #>/pdata/1/2rr)
        3rrr  -->   the binary data of 3D
        (Directory : /<diskname>/data/<username>/nmr /filename/<expt #>/pdata/1/3rrr)
      2. data analysis
        Aurelia <name>
        [Process 4]  -->   select 3D data (Process 1   -->   select 2D data)
        [View planes]   -->   view 3D planes
        [Strip edit]  -->  plot 3D data peak

    ( refer to http://www.bruker.de/analytic/nmr-dep/nmrsoftw/prodinfo/au_home/main.html )
     
  • nmrDraw :
    1. Purpose:
        NMRDraw is the companion graphical interface for NMRPipe and its processing tools. Features of NMRDraw include:
      • Interactive interface for inspecting 1D-4D FIDs, interferograms, and spectra.
      • Real-time manipulation of one or more 1D vectors within the viewed data, including pan, zoom, vertical scaling and offset, with 1D spectral graphics overlaid on 2D contour display.
      • Real-time phasing of one or more vectors for any dimension, with imaginary data reconstructed automatically as needed.
      • Facilities for interactive processing of individual vectors, and a script editor for construction of processing schemes.
      • Interactive peak editing, with an interface to automated 1D-4D peak detection via NMRWish.
    2. Using nmrDraw
        STEP :
      1. prepare data sets
        Nmrpipe processed data format files include
        *.ft (2D) and *xyz%3d.ft (3D) files   -->  nmrpipe generate processed data sets
      2. data analysis
        nmrDraw
        [files] read *.ft   -->   view the nmrpipe processing 2D or 2D plane of 3D data

    ( refer to http://spin.niddk.nih.gov/bax/software/NMRPipe/info.html )
     
  • nmrView   (analyze NMR data) :
    1. Purpose:
        NMRView is a program for the visualization and analysis of NMR datasets. The following summarizes some of the features of NMRView.
      • Multiple views on one or more NMR spectra. Unlimited number of spectral windows.
      • Windows may be in any size or position on the screen. Unlimited number of data files.
      • Generic reader for block structured files. Corresponding cursors in different windows track each other automatically.
      • Contour plots of any plane of any 2, 3, or 4 dimensional spectra. 1D vector plots ina any orientation of 1 to 4 dimensional spectra.
      • Spectral displays may be transferred from one window to another using a Copy/Paste protocol.
    2. Using nmrView
        STEP :
      1. prepare data sets
        Nmrpipe processed data format files include
        *.ft (2D) and *xyz%03d.ft (3D) files   -->  nmrpipe generate processed data sets
      2. data conversion
        xyz2pipe -in hnco%03d.ft -x > hnco_3D.ft
      3. data analysis
        nmrView
        [files] read *.ft   -->   view the nmrpipe processing 2D or 2D plane of 3D data

    ( refer to http://www.nmrview.com/ )
     
  • Sparky
    1. Purpose:
      Sparky displays contoured 2, 3, and 4 dimensional frequency domain spectra. It does not have facilities for viewing 1-D spectra and it will not read FID (free induction decay) data. You must first fourier transform the time domain FID data using a processing program.You can pick, assign, and integrate peaks using a graphical interface to . You can work with any number of 2-4 dimensional spectra simultaneously. The program has been developped to assist in structure determination of proteins, DNA and RNA.
    2. Using Sparky
        STEP :
      1. prepare data sets
        XWINNMR processed data format files include
        2rr  -->   the binary data of 2D
        3rrr  -->   the binary data of 3D
      2. data conversion
        Depends on the kind of processed data need to convert to UCSF format
        bruk2ucsf 1/pdata/1/2rr noesy150.ucsfBruk2ucsf   -->  convert bruker format to ucsf format
      3. data analysis
        sparky
        [file]  -->   select nmr data set and adjust the spectrum counter and peak picking
        [extensions]   -->  views   -->   strip plot   -->  select peak and plot for assign backbone

    ( refer to http://www.cgl.ucsf.edu/home/sparky/manual/manual.html )
     

Structure Calculation software

  • CSI Chemical Shift Index   (making consensus plot) :
    1. Purpose:
      The Chemical Shift Index or CSI is a quick and robust way of deriving secondary structure information from chemical shift data. The chemical shifts of HA, CA, CB and CO can be compared to their random coil values and then assigned with an index of 1 (beta sheet), 0 (coil) or -1(helix). If you have 3 or more types of shift for a particular residue then a concensus secondary structure for your protein will be calculated.
    2. Using CSI
        STEP :
      1. prepare data sets
        chemical shift file residue name, seq ID, atom type, chemical shift
      2. generate data from CSI
        CSI  -->   a menu should then appear to select
        > input chemical shift files
        > output file
        > display output graphics

    3. ( refer to http://www.pence.ualberta.ca/ftp/csi/ )
       
  • TALOS (Torsion Angle Likelihood Obtained from Shift and sequence similarity)  (dihedral angles prediction) :
    1. Purpose:
      TALOS is a database system for empirical prediction of phi and psi backbone torsion angles using a combination of five kinds (HA, CA, CB, CO, N) of chemical shift assignments for a given protein sequence. The TALOS approach is an extension of the well-known observation that many kinds of secondary chemical shifts (i.e. differences between chemical shifts and their corresponding random coil values) are highly correlated with aspects of protein secondary structure. The goal of TALOS is to use secondary shift and sequence information in order to make quantitative predictions for the protein backbone angles phi and psi, and to provide a measure of the uncertainties in these predictions.
    2. Using TALOS
        STEP :
      1. prepare data sets
        chemical shift table files    residue name, seq ID, atom type, chemical shift
      2. generate data from talos
        talos.tcl -in myshifts.tab  -->   Run TALOS (talos.tcl) to perform the database searches.


    3.  
  • XPLOR   (structure calculation) :
    1. Purpose:
      As mentioned in the Introduction, X-PLOR supports different protocols for structure calculations. These typically are:
      1. distance geometry combined with simulated annealing (dgsa)
      2. simulated annealing (sa)
      3. 3) simulated annealing using torsion-angle dynamics (tad)
      We will use here the second protocol (sa). Before starting the calculations you need first to generate a topology of your molecule and a starting structure. This has been described in chapter 4 under "Generating a starting structure".
    2. Using XPLOR
        STEP :
      1. prepare data sets
        1. chemical shift table files    residue name, seq ID, atom type, chemical shift
        2. protein structure files
        3. NOE tables    peak #, 15N ppm, NH ppm, H ppm, Int., Vol
        4. NOE table (assigned)
        5. J-coupling data
        6. H-bond file
        7. sequence files
        8. pdb files
        9. others
      2. generate data from xplor
        > xplor < my_input_script > my_output_file

    3. ( refer to http://xplor.csb.yale.edu/xplor/ )
       
  • CNS   (structure calculation) :
    1. Purpose:
      Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing structure determination programs the architecture of CNS is highly flexible, allowing for extension to other structure determination methods, such as electron microscopy and solid state NMR spectroscopy. CNS has a hierarchical structure: a high-level hypertext markup language (HTML) user interface, User-friendly task-oriented input files are available for nearly all aspects of macromolecular structure determination by X-ray crystallography and solution NMR.
    2. Using CNS
        STEP :
      1. prepare data sets
        1. pdb file
        2. chemical shift file    residue name, seq ID, atom type, chemical shift
        3. NOE table    peak #, 15N ppm, NH ppm, H ppm, Int., Vol
        4. NOE table (assigned)
        5. J-coupling data
        6. H-bond file
        7. others…
      2. data conversion
        Convert all raw data to aria.tbl formate    awk.inp files have done
      3. generate data tree and path from html file
        cns.html  -->   give correct path for raw data (converted)  -->  new.html
        cns  -->   generate a working “project” including all information
        (ex: making cns1 )
        cns.html  -->   edit parameters for structure calculations  -->  run.cns
        cns  -->   “auto NOE assignment” and generate structures
        (under the /cns1/ directory)

    3. ( refer to http://cns.csb.yale.edu/v1.0/ )
       
  • ARIA   (structure calculation) :
    1. Purpose:
      ARIA is a software for automated NOE assignment and NMR structure calculation. It speeds up the NOE assignment process through the use of ambiguous distance restraints in an iterative structure calculation scheme.
    2. Using ARIA
        STEP :
      1. prepare data sets
        1. sequence file    3 letter code
        2. chemical shift file    residue name, seq ID, atom type, chemical shift
        3. NOE table  peak #, 15N ppm, NH ppm, H ppm, Int., Vol
        4. NOE table (assigned)
        5. J-coupling data
        6. H-bond file
        7. others……
      2. data conversion
        Convert all raw data to aria.tbl formate    awk.inp files have done
      3. generate data tree and path from html file
        aria.html  -->   give correct path for raw data (converted)   -->  new.html
        aria  -->   generate a working “project” including all information
        (ex: making run1 )
        aria.html   -->   edit parameters for structure caliculations   -->  run.cns
        aria  -->   “auto NOE assignment” and generate structures
        (under the /run1/ directory)

    3. ( refer to http://dodo.nmr.embl-heidelberg.de:9673/EMBL/Aria)
       

Structure display analysis software

  • PROCHECK   (structure analysis, ex. Ramachandra Plot) :
    1. Purpose:
      PROCHECK is to assess how normal, or conversely how unusual, the geometry of the residues in a given protein structure is, as compared with stereochemical parameters derived from well-refined, high-resolution structures.
    2. Using PROCHECK
        STEP :
      1. prepare data sets
        pdb file
      2. generate data from sequence file
        > procheck filename [chain] resolution

    3. ( refer to http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html )
       
  • GRASP   (surface charge) :
    1. Purpose:
      Grasp is a graphics program written for Silicon Graphics computers that is widely used by the structural biology community to visualize macromolecules.
    2. Using GRASP
        STEP :
      1. prepare data sets
        pdb file
      2. generate image data from sequence file
        > grasp sequence files

    3. ( refer to http://honiglab.cpmc.columbia.edu/grasp/ )
      ( refer to http://www.accelrys.com/products/ )
       
  • MOLMOL :
    1. Purpose:
      MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on Nuclear Magnetic Resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface. The display possibilities include conventional presentations, as well as novel schematic drawings, with the option of displaying different presentations in one view.
    2. Using MOLMOL
        STEP :
      1. prepare data sets
        pdb file
      2. generate image data from sequence file
        molmol
        [file]  -->  read mol   -->  PDB  -->  read sequence files

    3. ( refer to http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ )
       
  • INSIGHT II :
    1. Purpose:
      Insight II is a 3D graphical environment for molecular modeling. Its powerful user interface enables the seamless flow of data between a wide range of scientific applications. The Insight II environment integrates builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences.
    2. Using InsightII
        STEP :
      1. prepare data sets
        sequence file    3 letter code
      2. generate image data from sequence file
        insightII
        [Biopolymer]   -->  read   -->  read sequence files
        Build and modify molecular models of nucleic acid compounds.

    3.  
  • VINCE   (for NOE connectivity plot) :
    1. Purpose:
      VINCE -- for VIsualization of Nuclear ConnEctivity -- is a computer program for generating graphs summarizing nuclear Overhauser effects (NOEs) observed in proteins, in a form that is commonly used for publication. In addition, Vince can display secondary structure assignments, calculate and display chemical shift indices, or display other user-supplied data. Data are accepted in a variety of file formats, and the program permits interactive data entry. Some simple error-checking is performed on NOE data input files, and a brief sequence summary is provided. Vince generates PostScript output;
    2. Using Vince
        STEP :
      1. prepare data sets
        1. sequence file
        2. chemical chift files
        3. NOE table
      2. generate image data from sequence file
        vince
        [read sequence]  -->  read   -->  read seuqence files

    3. ( refer to http://www.rowland.org/rnmrtk/vince.html )
       
  • MOLSCRIPT :
    1. Purpose:
      MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
    2. Using molscript
        STEP :
      1. prepare data sets
        pdb file
      2. generate image data from sequence file
        molscript

    3. (refer to http://www.avatar.se/molscript/ )
       

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