You are here:

Help: New Experiment

Here, you can find help on how to setup and submit a new experiment.
General Information
  • Please note that your session data is lost as soon as you close the browser window/tab
    or you change your IP address!
Prepare Dataset

General Information

  • Upload all protein structure files that you want to compare with each other. Please note that the maximum number of files to be uploaded is for All-against-All comparison, and for All-against-Target comparisons, with a maximum size of MB per upload.
  • Add or delete files, or decompose protein structures into their models/chains
  • Press the PROCEED button in order to confirm your set of active chains.

Defining the Dataset

  • Protein structure files are accepted in PDB format and can be uploaded either as a file from the local hard disk or from the RCSB repository. Accepted file types: .PDB, .ENT, .BRK
  • Uploading a local file, this can be either a plain text file or compressed with zip, gzip, bzip2 or compress. It is also possible to upload a bundle of files packed as a zip or tar-ball archive.
  • Entering a valid PDB code, this will download the protein structure file from the RCSB repository. It is possible to specify a set of PDB codes, separated by spaces or commas.
    A chain can be specified directly after the PDB code. The chain identifier can be either a letter (e.g. 'B') or a number (e.g. '2'). The default (first) chain is specified by an underscore ('_'), all chains by an asterisk ('*').
    A different model than the first one can be specified after the chain with a hyphen in between (e.g. '-2').
    If a chain and/or model identifier is given, the PDB file will be split automatically into the corresponding chain/model.
  • A list file containing multiple PDB codes can be uploaded for convenience. This must bear the suffix 'LIST'.

Additonal Data

  • Pre-computed similarity matrices can be uploaded directly in order to make them available for comparison with ProCKSI's results. They must contain the same number of structures in the same order as the uploaded structures. Accepted file types are:
    • DM (distance matrix): 0 (most similar) - infinity (least similar)
    • SM (similarity matrix): infinity (most similar) - 0 (least similar)
    • NDM (normalised distance matrix): 0 (most similar) - 1 (least similar)
    • NSM (normalised similarity matrix): 1 (most similar) - 0 (least similar)
    • SDM (ProCKSI's standardised distance matrix): same properties as NDM
Calculation Manager

General Information

  • Select all Tasks that you want to be performed.
  • Alter the Task Parameters or use the default values.

USM Equations

USM1  =   
   max{ C(s1.s2) - C(s2), C(s2.s1) - C(s1) }   

max{ C(s1), C(s2) }
USM2  =   
   C(s1.s2) - min{ C(s1), C(s2) }   

max{ C(s1), C(s2) }
USM3  =   
   min{C(s1.s2), C(s2.s1) } - min{ C(s1), C(s2)}   

max{ C(s1), C(s2) }
Submission Manager

General Information

  • Give a Description of your experiment in order to identify it more easily afterwards.
  • Enter your Email Address so that you can be contacted when your experiment has been completed.