[phenixbb] refining a covalent-bound ligand

Nigel Moriarty nwmoriarty at lbl.gov
Thu Feb 22 09:35:40 PST 2018


Sebastiano

As Pavel said, send me the inputs if you are having issues.


Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Thu, Feb 22, 2018 at 9:25 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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 <+39%2002%209437%205167>
> fax +39 02 9437 5990 <+39%2002%209437%205990>
> web http://is.gd/IEOXtalUnit
>
>
>
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