[phenixbb] refining a covalent-bound ligand

[Christian Roth]

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


Am 26.02.2018 um 10:45 schrieb Sebastiano Pasqualato:
> 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 <nwmoriarty at lbl.gov 
>> <mailto:nwmoriarty at lbl.gov>> 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 : NWMoriarty at LBL.gov 
>> <mailto: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!
>>
>>     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 <tel:+39%2002%209437%205167>
>>>     fax +39 02 9437 5990 <tel:+39%2002%209437%205990>
>>>     web http://is.gd/IEOXtalUnit
>>>
>>>
>>>
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