Sebastiano
As Pavel said, send me the inputs if you are having issues.
Cheers
Nigel
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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Thu, Feb 22, 2018 at 9:25 AM, Pavel Afonine
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
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