[phenixbb] Sugar refine in phenix
Jan van Agthoven
janccp4 at gmail.com
Sun Nov 4 18:35:03 PST 2012
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>:
> 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
> 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?
>> 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
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