On Thu, Aug 18, 2011 at 5:41 AM, Huw Jenkins <[email protected]>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.) -Nat
