On 06/07/13 00:49, Wei Shi wrote:
Hi guys,
I was trying to view the simulated annealing omit map generated by Phenix
in Coot. When I opened resolve_composite_map.mtz and *_ed.pdb in Coot,
I could only see one monomer of the protein. It should be two dimers
of the protein plus two pieces of DNA. And when I opened the *_ed.pdb
in pymol, it showed the right thing: two dimers of the protein plus
two pieces of DNA. It seems that something in *_ed.pdb file is not
recognized by Coot. When I opened *_ed. pdb with text file and found
out that the word "break" is used instead of "ter" between different
chains, so I replaced all "break" with "ter", but this didn't help....
I don't know whether any of you had this before and would have any
suggestions for me. Thank you so much!
Hi Wei,
AFAICS, "BREAK" is not a valid PDB file token and I am surprised that a
Phenix PDB file writer would generate such a thing. Coot (and many CCP4
programs) will read the file up until the BREAK token and provide the
atoms that it has read until then.
If you do not have SEQRES records, you can try deleting your BREAK
records from the file (grep -v BREAK) and you should get what you want.
Regards,
Paul.
