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Software Packages (with online help)

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NMR Data Processing and Analysis

    CARA

  • A program for assignment of NMR resonances in biomacromolecules. Except NMRView format, variety of formats of NMR spectra can be opened, processed and analyzed.
  • Learn more by visiting program's website and reading the tutorial
  • Type cara at the command prompt to run this program

    CcpNmr

  • CcpNmr is an analysis program built on top of the CCP Data Model. NMR spectra of different formats (NMRView, Sparky, NMRPipe) can be analyzed without any problem.
  • Online tutorials are here
  • Type analysis at the command prompt to start ccpnmr analysis program

    nmrPipe

  • A widely used tool to process the 2D & 3D NMR datasets
  • nmrPipe Website gives more information.
  • Some useful model scripts for the beginners can be seen here

    nmrPipe Accessory Programs

  • Companion Programs for nmrPipe package

    NMRViewJ

  • A program for the visualization and analysis of NMR datasets
  • Click here to see the step-by-step procedure to assign a protein using NMRViewJ
  • To run this program type nvj on any terminal.

    PINE-SPARKY

  • A program that uses the sequence of a protein in conjunction with peak lists from a variety of NMR experiments to generate the automatic backbone and sidechain assignments
  • Online tutorial and reference manual can be found here
  • Upload your peaklists and sequence information here

    SPARKY

  • A graphical NMR assignment program for proteins, nucleic acids, and other polymers
  • Step-by-step instructions to assign a protein is given here
  • Type sparky in any terminal to start this program Bar Break


    Structure Calculation & Secondary Strcuture Determination

    ARIA

  • A software for automated NOE assignment and structure calculation using ambiguous distance restraints.
  • See the tutorial on starting an ARIA calculation with PIPP data

    PECAN

  • Secondary structure identification for well defined regions
  • Download this conversion script to generate a NMR-STAR input supported by PECAN

    XPLOR-NIH - NMR macromolecular structure determination

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    Displaying and Analyzing Molecular Structures

    Chimera

  • Program for interactive visualization and analysis of molecular structures and related data.
  • Visit the Chimera webpage and the tutorial page for more information.
  • Type chimera to start the program.

    dssp

  • Defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format
  • Type dssp at the command prompt and follow the instructions.

    MolMol

  • Graphical display of 3D structures, especially useful for handling simultaneous multiple models as is typically the case in NMR-based structure calculations

    PyMOL

  • Graphical display of 3D structures - A user-sponsored molecular visualization system on an open-source foundation.

    PROCHECK-NMR

  • A program to check the stereochemical quality of ensembles of macromolecular structures determined by NMR spectroscopy

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    Relaxation Data Analysis

    gridsrch

  • Iterative program to calculate correlation times from T1, T2 and NOE data
  • Type gridsrch to start the program

    ModelFree

  • Modeling of NMR Relaxation Data

    quick

  • Utility to calculate T1 & T2 from NMR peak internsities
  • To run type quick from any terminal

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    General LINUX utilities

    convert

  • A program for converting various graphical formats: rgb->jpeg etc.
  • Usage : convert file.gif file.jpeg

    ksnapshot

  • A program for screen capture on the kubuntu workstations

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Last updated on June 17, 2014