On 18/08/11 16:36, Nat Echols wrote:
On Thu, Aug 18, 2011 at 5:41 AM, Huw Jenkins <h.t.jenk...@leeds.ac.uk
<mailto:h.t.jenk...@leeds.ac.uk>> wrote:
Having spent a while on the CCP4bb trying to fix what I thought
was a Coot library problem but turned out to be an issue with the
input pdb file, and as was suggested by the original poster on the
bb, it would be useful if Coot could correct the syntax of nucleic
acid upon reading pdb files so that it matches the dictionary and
real-space refinement works.
Given that Coot used by default to change nucleic acid to the old
(Ur etc) format and standard-residues.pdb is in the old format
some of the code to do this must already be there?
My apologies for suggesting non-Coot solution, but the command
iotbx.pdb_remediator
in Phenix will convert the atom names to 3.2 format - perhaps this
would work as a temporary solution? (All of the code is freely
available, if Paul et al. want to re-use any of it - it has no
additional dependencies.)
Thanks for that, Nat.
We've [1] known that we need a program of this kind for a while now - we
knew that this sort of thing would be an issue when we upgraded the
dictionary. We don't have a solution available today.
So I endorse this solution. (I doubt that I will introduce this
functionality into Coot any time soon.)
Cheers,
Paul.
[1] various CCP4 people.
