[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):
http://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles
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!
Pavel
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
>
>
>
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