[phenixbb] Sugar refine in phenix
nwmoriarty at lbl.gov
Mon Nov 5 08:29:08 PST 2012
Currently, PHENIX doesn't put the LINK records in the output PDB. There
are arguments for and against so maybe that will change.
On Sun, Nov 4, 2012 at 6:35 PM, Jan van Agthoven <janccp4 at gmail.com> wrote:
> Hi Nigel ,
> Thanks for our help. It worked nicely. However, how do you make the
> covalent links appear in the pdb file?
> 2012/11/2, Nigel Moriarty <nwmoriarty at lbl.gov>:
> > Jan
> > You can create the required file using
> > phenix.ligand_linking model.pdb
> > The one or two output files should be passed to phenix.refine.
> > Don't hesitate to contact me if this is unclear or you encounter more
> > problems.
> > Nigel
> > NB. Any files sent to me will be held in strictest confidence.
> > On Fri, Nov 2, 2012 at 1:53 PM, Jan van Agthoven <janccp4 at gmail.com>
> >> Hi everyone,
> >> This is a basic question. I would like to refine the sugar ends of my
> >> protein. The sugar polymers are made of NAG and BMA and whenever I use
> >> phenix.ready_set and subsequently phenix.refine it results in a
> >> structure of disconnnected sugar monomers. Indeed the cif file
> >> generated by
> >> phenix.ready_set does'nt give any geometry constraints for connecting
> >> the monomers. How do create a cif file that tells phenix.refine how to
> >> refine the sugars?
> >> Thanks,
> >> Jan
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> > --
> > Nigel W. Moriarty
> > Building 64R0246B, Physical Biosciences Division
> > Lawrence Berkeley National Laboratory
> > Berkeley, CA 94720-8235
> > Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
> > Fax : 510-486-5909 Web : CCI.LBL.gov
> phenixbb mailing list
> phenixbb at phenix-online.org
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb