[phenixbb] refining a covalent-bound ligand

Pavel Afonine pafonine at lbl.gov
Thu Feb 22 09:25:30 PST 2018

Hi Sebastiano,

if the ligand in PDB file is placed correctly and distance between atoms 
that are supposed to have a bond is within reasonable then it should be 
linked automatically. Otherwise you can use custom bonds as described 
here (available in GUI and command line):


Phenix does not recognize LINK records.

To verify the link, check .geo file that lists all the restraints used 
in refinement.

Let us know if you more questions or need help!


On 2/22/18 05:13, Sebastiano Pasqualato wrote:
> Hi there,
> I have a pretty basic question.
> I am refining a structure in which a drug has been covalently linked 
> to a Cys of the protein.
> I have generated the .cif fie for the ligand, but I don’t know how to 
> tell the program that carbon C04 has to be covalently linked to the SG 
> of the Cys. Is that sufficient to insert a LINK record in the pdb 
> file? What is the correct syntax for that?
> Thanks a lot for the feedback and sorry for the naive question,
> ciao,
> Sebastiano
> -- 
> *Sebastiano Pasqualato, PhD*
> Crystallography Unit
> Department of Experimental Oncology
> European Institute of Oncology
> IFOM-IEO Campus
> via Adamello, 16
> 20139 - Milano
> Italy
> tel +39 02 9437 5167
> fax +39 02 9437 5990
> web http://is.gd/IEOXtalUnit
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20180222/07255b77/attachment.htm>

More information about the phenixbb mailing list