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

PDB-REDO / dssp

Application to assign secondary structure to proteins

BSD 2-Clause "Simplified" License

166 stars 19 forks source link

PDB input: parse error at line 1: This file does not seem to be an mmCIF file #48

Closed yunxiangz closed 1 year ago

yunxiangz commented 1 year 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?

drlemmus commented 1 year ago

Could you send us the input file so we can test

yunxiangz commented 1 year ago

Hi drlemmus,

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

6ymw_B.pdb.zip

drlemmus commented 1 year ago

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.