Topology Independent Comparison of Biomolecular 3D Structures

  • Q. How is the PDB database stored and used by CLICK. How regularly is the database updated ?
    Q.1(a) Database location

    To make search faster, CLICK uses a locally stored copy of the PDB database. This is done to avoid fetching the structures from remote PDB database and hence save time.
    Q.1(b) What is the frequency of updating the local database ?

    The local copy of the database used by CLICK is synchronized with the latest snapshot of the PDB database every week (on Sunday at 01:30 AM, Indian Time Zone). Due to the 1 week window between successive update of the local database, sometimes, it can happen that the PDB code entered by the user is not found by the server and the server will show an error saying that the 'PDB structure not found'
    Solution

    If you are sure that you have entered a correct the PDB code and the server is still reporting the 'PDB structure not found' error, then we suggest that you upload the structure rather than specifying the PDB code. This can happen when the local copy of the database is yet to be synchronized with the remote servers.

  • Q. Are there any worked out examples to help me understand the output of CLICK ?
    Yes, there are. See examples page.

  • Q. How to specify the fragments of a PDB structure ?
    The fragments can be specified in the following manner:
    • 1ang- The whole structure 1ang.
    • 1ang,A- The structure 1ang, chain A
    • 1xxa,A,B- The structure 1xxa, chains A and B
    • 1ang,A(1:15),A(82:100)- 2 fragment structure constituting residues 1-15 and 82-100 of the structure 1ang, chain A.

  • Q. Why are the alignment files (pir format), residue wise equivalence files (clique format) and details about the database search not displayed ?

  • Q. The number of structures reported in the database search result is less than the size of database ?
    For available databases, for example Human Protein, RNA, DNA etc. the PDB/chains are updated to remove obsoleted structures from the database. Obsoleted entries in the database are replaced by the updated structures in the PDB database.

    For user uploaded database, the number of results shown may be less than the actual number of entries in the database file (uploaded by the user) when the there are obsolete PDB entries. Users are requested to pre-check for obsoleted PDB entries.

  • Q. How to solve and interpret different types of errors shown by the server ?
    Below is a description of the different types of errors shown by the server,

    • Error: Chain identifier not found


      This error means that while extracting the PDB structure from the database, CLICK was unable to find the particular main chain identifier in the PDB file.

      Example:
      Input: 1TIG,F
      CLICK will try to extract all the amino acid residues in the main chain 'F' of the PDB structure, if it can not find the chain identifier ('F') then it will show the above error.

    • Error: Amino acid residue position not found


      This error means that while extracting the specific amino acid residues from the PDB structure, CLICK was unable to find one or all of the residue positions.

      Example:
      Input: 1TIG,A(1:10)
      CLICK will try to extract the amino acid residues between positions 1 and 100 (including both 1 and 100) in main chain A of PDB 1TIG, if the psitiosn 1 or 100 are not present in the PDB then CLICK will show the above error.

    • Error: PDB structure not found


      This error means that the PDB structure specified by the user does not exist in the local copy of the PDB database. CLICK will never report this error for uploaded PDB structures. If you are sure that you have entered the correct 4 letter PDB code then it means that the local copy of the PDB database do not have that specific structure.

      Solution: If the structure entered by the user is recent (less than 1 week old) then the chances are that CLICK will not find it in the local database. We suggest that you download the structure from PDB database and upload it in CLICK.

    • Error: Representative atom not found


      This error means that while extracting the PDB structure from the database, CLICK was unable to find the particular representative atom(s) in the PDB file. Please separate multiple representative atoms by space.

      Example:
      Input: 3HGA Representative Atom: CA
      CLICK will check the PDB structure for 'CA' atom, if it can not find the representative atom then it will show the above error.

    • Error: Fragment range does not contain minimum number of atoms/amino acid residues


      CLICK need at least 3 representative atoms to do the alignment (please see the CLICK Publication to understand how cliques are defined). This error means that the fragments specified by the user does not contain at least 3 representative atoms.

      Example:
      Input: 1TIG,A(83:84)
      Representative atom:CA
      The above residue range (83-84) contains only 2 CA atoms in the main chain 'A', so CLICK will report the above error.


  • Q. How to use the web server ?
    It's very easy. Just click on the '

    ' symbol on the extreme right hand side of the CLICK main page. This will start an automated tour of the web server. You can forward, pause or rewind the tour as per your convenience.

  • Q. How long are the results of CLICK search (pairwise alignment and database alignment) stored by the server ?
    The results for pairwise and database search will be stored for a period of 7 days. After this time, the results will be purged by the server. User should download the result files (pairwise residue equivalence file, PIR alignment file etc.) for later reference.

  • Q. You have a question/doubt that is not addressed in the above list.
    Please contact us regarding your query by sending an email at Contact us.