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mittinatten / freesasa

C-library for calculating Solvent Accessible Surface Areas
http://freesasa.github.io/
MIT License
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Inserted residues #30

Closed OlekKuriata closed 6 years ago

OlekKuriata commented 6 years ago

For pdb files that contain residues numbered with both a number and a letter (inserted residues), the output pdb file contains those resides, but the generated RSA file only has one residue. I'm assuming they are all treated as one big residue, which might be an unexpected behavior.

Example lines from output pdb file: ATOM 2488 N ALA B 100 -5.419 26.119 30.440 1.65 0.18 ATOM 2489 CA ALA B 100 -3.963 25.990 30.448 1.87 0.44 ATOM 2490 C ALA B 100 -3.398 26.763 31.633 1.76 1.75 ATOM 2491 O ALA B 100 -4.033 27.686 32.136 1.40 0.00 ATOM 2492 CB ALA B 100 -3.379 26.543 29.155 1.87 0.00 ATOM 2493 N MET B 100A -2.209 26.376 32.085 1.65 0.34 ATOM 2494 CA MET B 100A -1.559 27.077 33.185 1.87 0.00 ATOM 2495 C MET B 100A -1.209 28.405 32.517 1.76 0.00 ATOM 2496 O MET B 100A -0.245 28.490 31.756 1.40 0.00 ATOM 2497 CB MET B 100A -0.320 26.296 33.615 1.87 0.03 ATOM 2498 CG MET B 100A -0.677 24.878 34.059 1.87 3.64 ATOM 2499 SD MET B 100A 0.715 23.813 34.483 1.85 0.46 ATOM 2500 CE MET B 100A -0.135 22.301 34.913 1.87 0.82

Output rsa: RES GLY B 99 0.10 0.1 0.00 N/A 0.10 0.1 0.10 0.2 0.00 0.0 RES ALA B 100 7.66 7.5 4.95 8.9 2.71 5.8 7.14 9.7 0.52 1.8 RES ASP B 101 5.22 3.9 2.23 2.5 2.99 6.6 0.00 0.0 5.22 6.4

mittinatten commented 6 years ago

Hi, thanks for reporting! Could you send me an example input file at (email address deleted), or post an excerpt with correct whitespace in this thread?

mittinatten commented 6 years ago

So the problem is the PDB ATOM field iCode is not read by FreeSASA. This should be fixed.

mittinatten commented 6 years ago

The commit cc480b3c3ac fixes this (dev branch).