(Logo) Using RasMol Scripts in the Course Material

  1. 1.1Kb GIF Browser window (27 Kb GIF)


    2. Hyperlinks to structure files are of two types: (a) those to structures which are part of the Brookhaven Protein Databank, and (b) to those which are not.

    (a) Where you see a series of links in this format:

    1mba (114Kb) [Bbk|BNL|ExP|Waw|Hal]

    they point to the same PDB file (in this example for the structure 1mba) in different copies of the Brookhaven Data Bank on the World Wide Web. Use the one closest to you. (Three of these sites also have the PPS Course on the same server.) Clicking on the link will download the PDB file stamped with the chemical/x-pdb MIME type (or chemical/pdb in the case of ExP) and so will automatically invoke RasMol, if you have your WWW Browser correctly configured.

    The key is as follows:

    BNL
    The Protein Data Bank itself at Brookhaven National Laboratories, USA
    Bbk
    The Crystallography Department, Birkbeck College, UK
    ExP
    ExPASy, the Experimental Protein Analysis System server at Geneva University Hospital, University of Geneva, Switzerland
    Waw
    Bioinformatics Unit of the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
    Hal
    Dept. of Biochemistry/Biotechnology, Martin-Luther-University, Halle, Germany
    (b) Structure files which are not part of the PDB are stored as local copies within the PPS Course material. This means that they are mirrored in 5 different sites: Birkbeck, Daresbury Laboratories (both UK), Brookhaven (US), Poznan (Poland) and Halle (Germany). These files have the .pdb extension. The Birkbeck Crystallography WWW Server is configured to serve all such files as chemical/x-pdb MIME. However, this may or may not be the case with the other PPS mirror sites. This means that if you are downloading the file from Brookhaven for example, it will be served as text. In this event, simply save a local copy on your disk, and then load it into RasMol before proceeding. (Note that the reason that these other servers such as Brookhaven PDB are not configured to stamp all files with a certain extension with chemical MIME is because sometimes it is desirable to access a text version of the file rather than downloading it straight into RasMol. Refer to Section 6 for further information.)
  2. 2.0Kb GIF Clicking on the link to the structure file should automatically invoke RasMol (22 Kb GIF)


    3. As explained above, if the structure file is NOT part of the actual PDB, and you are NOT accessing the Birkbeck PPS site, you will have to download the text-format file and load it into RasMol to proceed. However, most structures in the course material are in the Protein Data Bank.

  3. 2.2Kb GIF Copy and paste the script file into the RasMol command line window (28 Kb GIF)


    4. Raise the RasMol command line window, then click on the link to the script file. This will be delivered as text. Copy and paste the text into the RasMol command line window, to execute the commands.

    NB other protocols for serving RasMol scripts are possible, but these have been avoided so that multiple scripts may be used on the same structure, without having to download the PDB file each time. Refer to Section 6 for further information.

  4. 2.8Kb GIF RasMol executes the commands (24 Kb GIF)


    5. The scripts are aimed to be compatible with both versions 2.5 and 2.6 of RasMol. If you find any errors, please report them to pps2@mail.cryst.bbk.ac.uk


IndexIndex to Course Material

Last updated 11th Jun '96