Common errors

I submitted a query and received an error. What should I do?

Errors are most likely due to user's wrong input.
In the error email you have a list of all the parameters that you submitted to PROSS. Make sure that each parameter is correct.
Specifically, users who uploaded their own structure or MSA files often submit files that do not obey the formatting rules as described in our help boxes.

If you read the list below and have more ideas about errors to include here let us know.

Common user errors by submission parameters

  • Errors in PDB id (if you uploaded your own PDB file see a section below)
    1. The desired PDB id contains the letter 'o' but you typed the digit 0 or vice versa.
    2. Wrong PDB id - copy the id reported in the email and paste it in the RCSB web. Make sure it is indeed that protein you think it is.
    3. The PDB id is of a NMR structure. PROSS is not compatible with NMR structures unless you edit them and leave a single conformation.
    4. The PDB files contain negative residue numbers. Incompatible with PROSS.
    5. (rare) The PDB file contains a residue(s) for which one or more of the backbone atoms is missing. Note that if an entire residue is missing this is not a problem. However, if some atoms do exist, then all backbone atoms should also exist. To solve this problem remove all atom lines related to the problematic residue (i.e., turn it into a missing density).
  • Errors in Chain identifier to design
    1. Wrong identifier - not of a protein chain but of DNA or RNA chains.
    2. Wrong identifier - the identifier is of a protein chain but the wrong one and is incompatible with the rest of your parameters.
    3. Numerical identifier - PROSS is incompatible with numerical identifiers. You can change the identifiers in the structure file to letters and resubmit the query using the upload files option.
  • Errors in Small-molecule ligands
    1. Wrong identifier - either metathesis or maybe you are using a version of the name from the literature. Use the exact name as in the PDB file.
    2. Special ligand - for instance, the ligand is a free glutamate with the identifier 'E'. This is also an amino acid in proteins and PROSS does not know how to discriminate between the protein amino acids and the ligand. Edit the PDB file and change the ligand name; then use the upload files option to resubmit the query with the edited file.
  • Errors in Interacting chains
    1. An identifier was already used as the Chain identifier to design option.
  • Errors in Specific residues to fix
    Very common(!) and happens when one or more of the numbers does not exist in the PDB file. Common reasons:
    1. Typos
    2. A missing space leading to the merge of 2 numbers.
    3. Using a numbering scale from a paper or from a database that does not match the numbering scale in the PDB file.
    4. Trying to fix a position for which there is missing X-ray density.
    5. Specifying a number of a non-native amino acid that is not MSE/KCX/SCO.
    6. We suggest to open the PDB file on PyMOL and go over all the position numbers that you entered under this option. Make sure that you can select them on the designed chain in PyMOL. Free PyMOL version for students
      Command line example for selecting residues 120 and 121 by number on a designed chain A: select resi 120+121 and chain A
  • Errors in Uploading your own multiple sequence alignment
    The file should obey a strict format that is described near the upload box (click on the ? mark)
  • Errors in Upload your own PDB file and a Sequence file
    Errors in these options are common either due to wrong format of one of the files or due to incompatibility between the 2 files.
    Common errors:
      1. You uploaded an NMR solved PDB file or a PSE file (generated by PyMOL). These formats are not supported.
      2. The sequence file has a wrong format. Examples:
        1. There are no titles only sequence lines.
        2. The title lines have incorrect format. The correct one format is >A for instance, where A indicates that chain identifier
        3. The sequence lines contain: lowercase letters/non-amino acid letters (DNA/RNA,X etc)/Indels/special characters
      3. The sequences in the PDB file and in the sequence file do not obey PROSS rules. Common incompatibilities:
        1. The PDB file has amino acids that do not appear in the sequence file. For instance, the PDB file has a HIS-tag at the end that the FASTA sequence file does not show. Remember, the sequence in the sequence file should be equal or longer than the sequence in the PDB file.
        2. The are point mutations between that two sequences. This is not allowed. The only allowed mismatches are deletions in the PDB sequence (that represent lack of density)
      4. You've also uploaded a MSA file and the sequence file and the MSA or incompatible with each other. Read the help pages.
      5. One of the uploaded files has a character/sign that are not allowed. For instance, a whitespace before an ATOM line in the PDB file.
      6. One of the uploaded files has a hidden character that is not allowed. This often happens when preparing the files in a PC (windows) or when using rich text editors. Try to open your files in other editors or other operating systems (mac) to check if this is the case.
      7. The PDB file has lines in which the residue number includes also A-Z characters and not just numerical characters. This is often the case in antibodies but not only.
        For example: ATOM 2496 CA GLU C 114A 30.373 0.182 -56.367 1.00 29.68
        The bolded character fails PROSS. Assign a different number instead (a numerical residue number not used by other residues).
      8. See also the common errors in the PDB id option - your own files might suffer from some of them.

If you think that all the parameters are correct and yet the job fails, please contact us at