PDB input: parse error at line 1: This file does not seem to be an mmCIF file

Question

PDB input: parse error at line 1: This file does not seem to be an mmCIF file

Closed this issue 2 years ago · 3 comments

yunxiangz commented 2 years ago

Thanks for the outstanding work, I am new to the dssp!

I used the following command to process a PDB file:
/usr/local/bin/mkdssp ./xxx.pdb ./xxx.dssp

However, I got the following error:
parse error at line 1: This file does not seem to be an mmCIF file

Could you please help with the correct command for PDB inputs please?

Answer 1 · 2022-11-16T14:52:46.000Z

Could you send us the input file so we can test

Answer 2 · 2022-11-16T15:11:31.000Z

Hi drlemmus,

Thanks for your prompt reply! The file I tried is attached below:

6ymw_B.pdb.zip

Answer 3 · 2022-11-16T16:36:29.000Z

DSSP requires a valid mmCIF or PDB file as input. Your file is neither; it is a bunch of ATOM records. If you use a PDB file with at least a HEADER record and a CRYST1 record (the bare minimum, really), DSSP will see it as PDB file and should run properly. Without it, it assumes the default mmCIF format.