Re: [phenixbb] Sugar refine in phenix

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 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 :

...

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 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 _______________________________________________ phenixbb mailing list [email protected] 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

_______________________________________________ phenixbb mailing list [email protected] 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov