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

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