You could add the link description to your dictionary, import that in coot and it should work.

The non phenix way would be to create the link in jligand, write out the dictionary description and merge it with your ligand dictionary. The link statement needs to be in the pdb of course.

There might be also a way in phenix to do this, but I'm not aware of it at the moment. Maybe Pavel or Nigel can help out here.

Cheers

Christian

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.

Thanks.

Any idea on how to tell Coot the same things? ;-)

(I guess this one should go to the Coot_bb though ;-))

Thanks again,

ciao,

S

On 22 Feb 2018, at 18:35, Nigel Moriarty <[email protected]> wrote:

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 : [email protected]
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Thu, Feb 22, 2018 at 9:25 AM, Pavel Afonine <[email protected]> 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
fax +39 02 9437 5990

web http://is.gd/IEOXtalUnit

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