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MPI-Dortmund / pymissense

PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.
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Cant find chain #10

Open aspitaleri opened 4 months ago

aspitaleri commented 4 months ago

Hi there, thanks for the script! I am using to generate pdb with missense mutations. It works except for this:

pymissense O95477 abaca1 --maxacid 2224 --pdbpath 7tc0.pdb --tsv /tmp/alpha.tsv

Cant find chain for O95477 in 7tc0.pdb The pdb is from rcsb. Using --pdbpath 7TC0 it works. The chain is present and I tried also to keep only ATOM lines.

BTW, is it possible to get the tsv or the matrix used to generate the heatmap plot? To post process the data.

Best

thorstenwagner commented 4 months ago

Thanks for reporting this! I'm not in the office, but I will look into it when I'm back next week.

thorstenwagner commented 4 months ago

Quick comment: I downloaded the pdb from rcsb and I cant find uniprot id O95477 ?

aspitaleri commented 4 months ago

https://www.uniprot.org/uniprotkb/O95477/entry Using the --pdbpath 7TC0 it works. There is somethig weird in the rcsb file when downloaded first.