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haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.
https://haddocking.github.io/pdb-tools/
Apache License 2.0
372 stars 113 forks source link

Coot can't open the output file of pdb_merge #94

Closed 1ut closed 3 years ago

1ut commented 3 years ago 
pdb_merge a.pdb b.pdb ... > output.pdb
pdb_merge a.pdb b.pdb ... | pdb_tidy > output.pdb

I generated the output.pdb file like above(url of file: https://drive.google.com/file/d/1INUdZfA8dEoe40k0v4IA32iFHwI_JRno/view?usp=sharing) When I tried to open output.pdb using coot, it only showed the content of a.pdb file above. Howerver when I used Chimera, it showed the content of output.pdb. Next I saved the output.pdb file in chimera to another file (url of file: https://drive.google.com/file/d/1lpY40CnG3mXGZiXwQ96IBeNWYMN3Rkhd/view?usp=sharing). When opening it by coot, the content of output.pdb was shown.

I want to know how to generate file that can be used in coot by using this tool directly. Thanks in advance.

Coot version: 0.9.3

joaomcteixeira commented 3 years ago

Hi @1ut

I am removing the label bug until proven it is really a bug.

I am not aware of the Coot specifications but, you can try to remove the comment lines as they appear to be the main difference between the PDBs you sent, try:

pdb_merge a.pdb b.pdb ... | pdb_keepcoord | pdb_tidy > output.pdb

If that is not a problem to you, could you send us the original a.pdb and b.pdb so we can understand if there is really a bug? If those are private data of yours, never mind, we can try to sort it out together with you from here.

Cheers, and thanks for writing.

1ut commented 3 years ago

Pdb_keepcoord solved the problem. Thanks for prompt reply. 

pdb_merge a.pdb b.pdb ... | pdb_keepcoord | pdb_tidy > output.pdb