Parser.py has some issues

[jaideepm009]

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I believe "r" should be replaced with "current_resname" in line 452 of parser.py file under DockQ directory?

[jaideepm009]

But if i make the above change I get "Buffer has wrong number of dimensions (expected 2, got 1)". So I am not sure whats the issue.

[clami66]

Hi, could you attach the files you're trying to score?

[jaideepm009]

The files I am trying to process are 1cbv.pdb and the model file produced by rosettafold2 architecture. I am not able to attach them here :(

[clami66]

Try this:

1. Update the repository with git pull and rerun pip install
2. Since 1cbv contains a very small DNA molecule, it's likely that the short sequence is messing with the automatic mapping. So try to provide the mapping between native and model chains manually. It will be something like: --mapping ABC:DHL or similar (depends in what order Rosetta writes out the chains)

[jaideepm009]

I was providing chain map manually. I did git pull and reinstalled DockQ. I am still getting error in buffer dimension. Here are the screenshots of my code.

[clami66]

I cannot help you further without the model unfortunately. You should be able to make a zip, then drag and drop it in a comment box here on the issue

[jaideepm009]

Archive.zip

In model(model_00_pred.pdb): A corresponds to antigen chain, B corresponds to heavy chain, C corresponds to light chain. In native("1cbv.pdb): D = antigen, H = heavy, L = light. I need to calculate DockQ for antigen to heavy and antigen to light chains

[clami66]

Hi @jaideepm009

Chain A in your model is a peptide with unknown amino acids:

ATOM      1  N   UNK A   1     -14.695   1.700   8.805  1.00 33.72
ATOM      2  CA  UNK A   1     -16.016   2.020   8.281  1.00 33.72
ATOM      3  C   UNK A   1     -17.109   1.521   9.211  1.00 33.72
ATOM      4  O   UNK A   1     -17.328   0.316   9.344  1.00 33.72
ATOM      5  CB  UNK A   1     -16.594   1.112   7.207  1.00 33.72
ATOM      6  H   UNK A   1     -14.203   0.899   8.438  1.00 33.72
ATOM      7  HA  UNK A   1     -16.094   3.104   8.211  1.00 33.72
ATOM      8 1HB  UNK A   1     -17.641   1.395   7.016  1.00 33.72
ATOM      9 2HB  UNK A   1     -16.016   1.213   6.289  1.00 33.72
ATOM     10 3HB  UNK A   1     -16.562   0.078   7.547  1.00 33.72

But the native chain D is a NA (DNA?) molecule. So there is no way for DockQ to compare the two. The type of molecules need to be consistent across the two pdb files or it doesn't make sense to compare them

[jaideepm009]

Yes we just realised that yesterday as well! Thanks for taking the time out looking into the issue.