[phenixbb] autogenerate restraint.eff from PDB for phenix.varref
vincent Chaptal
vincent.chaptal at ibcp.fr
Fri Sep 15 07:43:05 PDT 2023
Hi Pavel,
yes I do have the file which goes :
geometry_restraints {
edits {
bond {
atom_selection_1 = chain A and resseq 1601 and name O2
atom_selection_2 = chain A and resseq 895 and name OG
distance_ideal = 3.2
sigma = 0.5
}
bond {
atom_selection_1 = chain A and resseq 1601 and name O2
atom_selection_2 = chain A and resseq 299 and name OG
distance_ideal = 2.3
sigma = 0.5
}
.... many more bonds....
}
}
But it takes some time to generate a good amount of restraints, and for
structures with several ligands it could be a long task.
Agreed that it is not fool-proof but a general edition of these bonds
and editing afterwards would be a good little program I believe.
Best
Vincent
Le 15/09/2023 à 14:34, Pavel Afonine a écrit :
>
> Hi Vincent,
>
>> Before launching phenix.varref, I would like to generate a ligand
>> restraint file so the ligand doesn't fly away from its density.
>> It would be great if the ligand_restraints.eff file could be
>> generated from a PDB file already containing the ligand (for example
>> originating from refinement), that we can then edit afterwards. The
>> ligand I'm talking about is ATP in this case, so it doesn't need
>> external cif file for refinement.
>>
>> I searched but couldn't identify such a job. It would be useful if it
>> could be added to "PDB tools" or similar.
>
>
> you need to define what in Phenix is called custom bond restraints:
> some "dummy" bonds between pairs of ligand and protein atoms of your
> choice. These bonds will anchor the ligand in place. Let me know if
> you need help setting up those but I think I sent you an example some
> time ago.
> While generating such a file automatically is possible it may not be
> fool-proof as it will depend on the geometric quality of the model. So
> it's best to use your chemical intuition to choose those pairs of
> atoms that you'd like to link.
>
> Good luck!
> Pavel
>
>
>
--
Vincent Chaptal, PhD
Director of GdR APPICOM
Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
http://www.appicom.cnrs.fr
http://mmsb.cnrs.fr/en/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20230915/30ce0d53/attachment-0001.htm>
More information about the phenixbb
mailing list