[phenixbb] Sugar refine in phenix

Jan van Agthoven janccp4 at gmail.com
Mon Nov 5 08:55:07 PST 2012


Ok, thanks!

Jan
2012/11/5, Nigel Moriarty <nwmoriarty at lbl.gov>:
> 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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>> >> 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
>> >
>> _______________________________________________
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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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