FAQ re PDBeFold

  • List of Pairs and Fileset.
    PDBeFold can accept a list of pairs (of file names) and a tar (gz) file containing these files.. The format is:

    > cat listofpairs.txt 
    2vvw_A.pdb 2vvy_C.pdb
2vvw_A.pdb 4lqk_B_core.pdb
2vvy_C.pdb 2vvw_A.pdb
2vvy_C.pdb 4lqk_B_core.pdb
4lqk_B_core.pdb 2vvw_A.pdb
4lqk_B_core.pdb 2vvy_C.pdb

> tar ztf fileset.tar.gz
2vvw_A.pdb
2vvy_C.pdb
4lqk_B_core.pdb
    PDBeFold displays the results of matching all structures in the first column against all structures in the second column.
  • Multiple Alignment - List of PDB entries.
    Here a list of PDB entries in a text file is uploaded and the entries compared against each other. The format of the file is

    > cat listofentries.txt 
    2AXI
1Z2U
2CNQ
2DPL
2DXU
2PHN
2PIE
2VOK
2X5O
3ASL
3BUX
  • Multiple Alignment - fileset.
    Here a tar file containing PDB files is uploaded and the entries compared against each other. The format of the file is:

    > tar ztf pdbfileset.tar.gz 
    pdb1z2u.ent
pdb2axi.ent
pdb2cnq.ent
pdb2dpl.ent
pdb2dxu.ent
pdb2phn.ent
pdb2vok.ent
pdb2x5o.ent
pdb3asl.ent
pdb3bux.ent
  • Browser
    The recommended browsers are Netscape 6+ and IE 6+. The server should work with all browsers that support a primitive Java scripting. Support of frames is not needed. Please make sure that your browser is set to not using the cache. Go to browser's preferences, section "Cache", and set comparison to the network as "Every time" or "Automatically".
  • Back and Forward Buttons.
    Uisngf the "Back" and "Forward" buttons in your browser while working with PDBeFold might produced unexpected results. All necessary navigation buttons are provided.
  • Calculation in progress pages.
    After submitting a query, the server displays a self-updating wait page showing the progress. If you do not see the progress: probably your browser reloads the wait page from the cache - please refer to section "Browser" above. If your browser does not allow switching the cache off, you will have to reload the wait page manually, e.g. by clicking on the "Reload" button of your browser.
  • Sending Multiple Requests.
    You may bookmark the wait page once it is displayed. This link would then take you either to results, if those are ready, or to the progress show. Even before your query finishes, you may submit another one by simply following the corresponding link in the wait page. Results expire in 4 hours.
  • Blank Wait Page.
    If the wait page goes blank or corrupted, simply press "Reload" button in your browser.
  • Data conversion There are some data conversion tools listed here: http://jeroenjanssens.com/2013/09/19/seven-command-line-tools-for-data-science.html This list is given withoput any guarantee as to completeness or suitability.