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Supported Applications

O

  • Description

    a model building application for X-ray crystallography.

  • Usage

    To list all executables provided by O, run: $ sbgrid-list o Copy to clipboard

  • Usage Notes

    As of version 12.0, O no longer requires a license file.

    To use custom O data files (rotamer database, interface files, etc), you must override the ODAT environmental variable to point to your own directory.

    • Open a tcsh new shell and source /programs/labcshrc
    • echo $ODAT (note the current O data directory
    • cp -Rp $ODAT ~/o_data (copy the current O data files to your home directory)
    • setenv ODAT ~/o_data (you can add this to your ~/.cshrc after the 'source /programs/labcshrc" line)

    Copy your custom files to ~/o_data and then run your newly customized O.

    O works with SGI Dials. If you're using OS X, you should download and install the most recent USB<->Serial adapter driver for dials use from David Gohara's website. The download file contains a PDF with instructions on installation and set up.

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install o Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    T. A. Jones, J.-Y. Zou, S. W. Cowan, and M. Kjeldgaard. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A Foundations of Crystallography. 47(2): 110-119.


    • *Full citation information available through

  • Tales

    Springsteen, Tolkien, Protein

    Springsteen, Tolkien, Protein

    An unexpected side-effect of Alywn Jones's decision to write Frodo, one of the first computer graphics programs written for Xray crystallography, was learning to swear in German. His teacher? Johann Deisenhoffer, the 1988 winner of the Nobel Prize in Chemistry.

    “He was always using my experimental versions,” said Jones, then at the Max Planck Institute for Biochemistry, now professor of structural biology at Uppsala University in Sweden. “He used to swear at me when my program exploded, which it often did.” Back then, in 1976, Jones had happened into computer graphics. “I took a wrong turn and I just kept going,” he says, his voice just slightly less gritty than that of The Boss.

    Jones programmed on what at the time was a sophisticated computer. “I could have …

    Read the full story here.

  • Keywords

    Crystallography, Visualization

  • Default Versions

    Linux 64:  15.0.0 (4.3 MB)
    OS X INTEL:  15.1.0 (4.1 MB)

  • Other Versions

      Linux 64:

      12.0.1 (2.4 MB) , 13.0 (3.2 MB) , 13.1.0 (3.8 MB) , 14.0.0 (4.0 MB)

    • OS X INTEL:

      10.0.3 (3.8 MB) , 11.0.2 (3.1 MB) , 11.0.4 (3.1 MB) , 12.0.0 (3.8 MB) , 12.0.1 (3.8 MB) , 13.0 (4.1 MB) , 14.0.0 (4.3 MB) , 15.0 (4.5 MB)
    • Common files size: 260.5 MB

  • Developers

    Alwyn Jones

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