[phenixbb] Sugar refine in phenix

[Nigel Moriarty]

Jan

Currently, PHENIX doesn't put the LINK records in the output PDB. There
are arguments for and against so maybe that will change.

Nigel

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?
> Thanks,
> Jan
> 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>
> wrote:
> >
> >> 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
> >> _______________________________________________
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> >>
> >
> >
> >
> > --
> > 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
> >
> _______________________________________________
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>



-- 
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
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