[Chimera-users] Pseudobonds in mmCIF

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 16 09:40:05 PST 2018

Just for the benefit of the list, the problem with spurious bonds between residues in Chimera was solved by adding sequence information to the input mmCIF file.

> > On Jan 11, 2018, at 1:35 PM, Henry Nguyen <nguyen.henry.c at gmail.com> wrote:
> >
> > Thanks everyone for all the help. My problem is fixed by running mmtbx.prepare_pdb_deposition with the sequence information. The new cif file is displaying pseudobonds correctly and can be toggled on/off.
> >
> > Thanks again!
> > Henry
> >
> > On Thu, Jan 11, 2018 at 11:43 AM, Greg Couch <gregc at cgl.ucsf.edu> wrote:
> > Hi Henry,
> >
> > Sorry about the problems with mmCIF in Chimera.  Those problems are a major reason why we wrote ChimeraX.  So please check out ChimeraX, http://www.rbvi.ucsf.edu/chimerax/.  The mmCIF reader is several orders of magnitude faster than Chimera's and presents the author numbering to identify residues instead of the internal mmCIF numbering.  The graphics in ChimeraX are better too.  If there is some feature in Chimera that isn't in ChimeraX yet that you need, please let us know.  ChimeraX also works with VR headsets.
> > And while ChimeraX shows your structure "correctly".  It could do a much better job if the missing sequence information were in the mmCIF file.  In Phenix, that is done by running the mmtbx.prepare_pdb_deposition program, i.e, by preparing the mmCIF file so that is suitable for submission to the PDB.  That would probably help Chimera too.
> >
> >     HTH,
> >     Greg

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