Question on `pdb_keepcoord`

[joaomcteixeira]

@JoaoRodrigues should pdb_keepcoord remove also the REMARK ? Below an example in comparison with grep ATOM.

(base) joao@vantito:~/projects/haddock/tmp
· pdb_fetch 4I1B | pdb_tidy -strict | pdb_delhetatm | grep ATOM | pdb_chain -B | pdb_chainxseg | pdb_tidy -strict >4I1B_clean.pdb
(base) joao@vantito:~/projects/haddock/tmp
· pdb_fetch 4I1B | pdb_tidy -strict | pdb_delhetatm | pdb_keepcoord | pdb_chain -B | pdb_chainxseg | pdb_tidy -strict > 4I1B_clean_B.pdb
(base) joao@vantito:~/projects/haddock/tmp
· diff 4I1B_clean.pdb 4I1B_clean_B.pdb
1,6d0
< REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
< REMARK   3   PROTEIN ATOMS            : 1207                                    
< REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
< REMARK   3   HETEROGEN ATOMS          : 0                                       
< REMARK   3   SOLVENT ATOMS            : 91                                      
< REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
(base) joao@vantito:~/projects/haddock/tmp

[amjjbonvin]

I would vote to indeed remove the REMARKS and any other lines not matching ATOM.

[joaomcteixeira]

I agree with you.

[JoaoRodrigues]

Yeah, keepcoord means, remove everything that's not a coordinate :) Sorry, only saw this one now!

[joaomcteixeira]

This is already addressed:

https://github.com/haddocking/pdb-tools/blob/f092906a985990661d1ec87b0efd0748e7f26289/pdbtools/pdb_keepcoord.py#L90-L95