Known Problems

There are a few submission problems you may face. Please try to follow the following guidelines.

(1). Please make sure that you have SEQRES records in the PDB file. The formatting should be same as the PDB file at http://www.rcsb.org/. If you do not have one, please go to http://proknow.mbi.ucla.edu/seqres.php and get your SEQRES records. If you can get the original sequence of the protein in FASTA format that will more accurately calculate the function than the one derived from the ATOM coordinates in PDB. SEQRES records derived from PDB may lack residues if there are chain breaks and amino acid modifications.

Please upload one model per chain for an NMR structure.

(2). If you are uploading a FASTA file, have a look at the example file. I have found people uploading files with sequence positions in them. Sometimes the file is also replete with ^M characters that stops the parser to read all the lines properly. If you are not sure what is the correct format, simply paste your sequence in the box. The minimum length of the sequence that will be worked on is of 25 residues.

(3). This server only accepts protein sequence. If you submit nucleotide sequence it will try to interpret T as Threonine, C as Cysteine, G as Glycine and A as Alanine!

(4). Always please upload files in text format. I have seen people uploading all sorts of different file formats for which I do not have any filters right now. In such cases the server will try to work with your files and probably send you a blank mail!

(5). Sometimes your submission may be perfectly OK, but the server may not still return any result. This could be due to the following reasons:

  • One of the programs bounced killing the rest of the job.
  • There is too much load on the server and there was an NFS failure.
  • Your job is too long and was terminated by the server. The maximum allowed time is 1 hour.
  • The local Linux cluster is down or has a large queue causing your job to go to an error state.
  • The MYSQL server has gone away.

    • (6). If you are submitting your job from a non UNIX/LINUX machine please check if the file is readable by Notepad. The end-of-line characters from Windows and Mac machines are treated differently by UNIX/LINUX systems and therefore the server, which is run under LINUX reades it as one single line.