Biopandas PDB output formatting leads to a ton of segments when reading with MDAnalysis: reason and my quick fix

[mrauha]

Hi all,

was a bit baffled opening biopandas PDB output with MDAnalysis. Instead of some dozen segments, I got thousands. Here's why & my hacky fix:

Biopandas outputs the rows in a following way:

ATOM  50786  CB  ASP q  96     219.123 233.404 332.880  1.00 97.39           C
ATOM  50787  N   PRO q  97     222.483 233.701 332.586  1.00 100.66           N

while in MDAnalysis expects this format:

ATOM  51419  O   UNK r 113     214.624 201.542 285.597  1.00 99.63           O
ATOM  51420  CB  UNK r 113     217.297 202.297 286.117  1.00100.32           C

Due to this formatting when B-factors have five numbers (>99.99), MDAnalysis parses the last digit of the B-factor to be the segid and uses them as chains, see the code for th eparser:
Line 297:

                segids.append(line[66:76].strip())

Lines 304-306:

        # If segids not present, try to use chainids
        if not any(segids):
            segids = chainids

As a quick fix, I commented out the last if statement in MDAnalysis.

[rasbt]

Thanks for the note, I think I've heard about this issue before. I think there was a similar issue with the atom number that I fixed many years ago. I think this issue can be fixed in a similar fashion. Just need to find the time for this some time. Thanks for pointing it out!