[phenixbb] refining a covalent-bound ligand
sebastiano.pasqualato at gmail.com
Mon Feb 26 02:45:54 PST 2018
Dear Nigel and Pavel,
thank you very much for you feedback and precious advice.
It is a compound with a C=C double bond that gets attacked by the S of a Cys, hence I think it’s normal that the program is not recognising automatically the bond.
I have changed the C=C bond to C-C and recreated the CIF file for the compound, than provided phenix the bond restrains (bond length and angles) for the C-S bond.
It all seems to work very nicely.
Any idea on how to tell Coot the same things? ;-)
(I guess this one should go to the Coot_bb though ;-))
> On 22 Feb 2018, at 18:35, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
> As Pavel said, send me the inputs if you are having issues.
> 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 <http://cci.lbl.gov/>
> On Thu, Feb 22, 2018 at 9:25 AM, Pavel Afonine <pafonine at lbl.gov <mailto: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 <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!
> 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 <tel:+39%2002%209437%205167>
>> fax +39 02 9437 5990 <tel:+39%2002%209437%205990>
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