Dear Roberto,
Roberto Steiner wrote:
Dear all,
a problem possibly at the coot/mmdb interface...
Indeed.
If one uploads a pdb file (from phenix.refine in the example below)
that contains Hs into Coot and then writes it out (with or without any
modification done on it) Coot shifts the HG2n of THR on the right by
one column space. Because column 17 is kept empty the result is three
identical HG2 THR protons.
Technical answer:
The current PDB parser in Coot is from mmdb and is for PDB format
version 2.3. Phenix.refine and other modern programs use PDB format
version 3.0 [1] - released over a year ago. PDB version 3.0
"Remediated" does not wrap the hydrogen (or other) names and so the
hydrogen name "unmangler" - which is what is tripping you up - need not
be executed. I'd like to make Coot compatible with the current PDB
standard. If CCP4 were to release a version of mmdb compatible with
Coot, I could do that right away [2]. I'm hoping that they will do so
today^H^H^H^H^H soon.
The only solution right now (that I know of) is to remove all Hs and
generate them again (molprobity for example) prior to refinement.
Bleugh. Non-optimal (no matter how fine Molprobity is).
Paul.
[1] or version 3.1?
[2] I imagine.
