Courtney Currently, the only way to check whether a bond is being made is to look in the .geo file produced by phenix.refine. I'm guessing that you are using a visual check in Coot after refinement to see if the ligand is bound. Coot is using LINK records in the PDB file which phenix.refine doesn't currently write so you can not use a visual clue to say that the bond was not formed in refinement. Coot is a different program and creates representations of bonds from different inputs. If you used PyMOL to view the model, the bond may have been drawn on the screen for you because PyMOL uses the distance between two atoms to draw a bond on the computer screen. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, 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 On Mon, Jul 27, 2015 at 8:29 AM, Courtney Daczkowski wrote:

We are currently trying to build a model that has a nonstandard ligand that is covalently bonded to two peptide chains. We've placed the ligand and linked it using Coot, but phenix.refine keeps removing the links. We generated the restraints using Elbow and wrote the .edits file using phenix.link_edits, but phenix.refine is still removing the links. We also tried turning on automatic ligand linking in phenix.refine, but that didn't work either. Any advice?

Thanks.

Courtney

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]