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mittinatten / freesasa

C-library for calculating Solvent Accessible Surface Areas
http://freesasa.github.io/
MIT License
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freesasa python bindings hang with unknown residues? #100

Open JavierSanchez-Utges opened 3 months ago

JavierSanchez-Utges commented 3 months ago

Hi, I have had trouble running the freesasa python bindings for a structure 6bcu, chain A. At first I thought it was because of the size. Then, I realised it was because some residues are not known and assigned UNK resName. I installed the command line program of freesasa and then ran it and got this on the standard error:

FreeSASA: warning: atom 'UNK  N  ' unknown, guessing element is ' N', and radius 1.550 A
FreeSASA: warning: atom 'UNK  CA ' unknown, guessing element is ' C', and radius 1.700 A
FreeSASA: warning: atom 'UNK  C  ' unknown, guessing element is ' C', and radius 1.700 A
FreeSASA: warning: atom 'UNK  O  ' unknown, guessing element is ' O', and radius 1.520 A
FreeSASA: warning: atom 'UNK  CB ' unknown, guessing element is ' C', and radius 1.700 A
FreeSASA: warning: atom 'UNK  N  ' unknown, guessing element is ' N', and radius 1.550 A
FreeSASA: warning: atom 'UNK  CA ' unknown, guessing element is ' C', and radius 1.700 A
FreeSASA: warning: atom 'UNK  C  ' unknown, guessing element is ' C', and radius 1.700 A
FreeSASA: warning: atom 'UNK  O  ' unknown, guessing element is ' O', and radius 1.520 A
...

All these residues then contribute to the UNKNOWN partition of the sasa. I think the python bindings might not know how to deal with this and just hang. It was running for hours on my Jupyter notebook, then running it on the command line was immediate.

I think it was also the case for: 6bq1_A and 7ktr_A if you want more examples.