[phenixbb] autogenerate restraint.eff from PDB for phenix.varref

[vincent Chaptal]

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

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