> 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@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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>>
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>>
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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@LBL.gov
> Fax :
510-486-5909 Web :
CCI.LBL.gov
>
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