[phenixbb] refining a covalent-bound ligand
pafonine at lbl.gov
Thu Feb 22 09:25:30 PST 2018
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
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,
> *Sebastiano Pasqualato, PhD*
> Crystallography Unit
> Department of Experimental Oncology
> European Institute of Oncology
> IFOM-IEO Campus
> via Adamello, 16
> 20139 - Milano
> tel +39 02 9437 5167
> fax +39 02 9437 5990
> web http://is.gd/IEOXtalUnit
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