[phenixbb] Help with custom bond restraints syntax

Pavel Afonine pafonine at lbl.gov
Thu Oct 21 08:52:44 PDT 2010

  Hi Jobi,

I hope Jeff has helped you already. So just as a remark of how you can 
quickly debug it...

Just type this from your command line:

phenix.pdb_atom_selection model.pdb "chain S and resid 501 and name C7"

and that will print the lines from PDB file that you have selected with 
the above atoms selection syntax.

Similarly do for another one:

phenix.pdb_atom_selection model.pdb "chain A and resid 25 and name SG"

If it doesn't print anything or complaints, that means that either your 
atom selection syntax is not right (which is NOT your case since it 
appears to me correct), or simply you are trying to select atoms that 
are NOT present in your PDB file (empty selection).


On 10/20/10 10:49 PM, Jobichen Chacko wrote:
>  Dear All,
> I am trying to make a custom covalent  bond with an inhibitor compound 
> and my protein. Plesae see the attached file for restraints file. But 
> phenix is returning this error. Please help.
> Sorry: No atom selected: 'chain S and resid 501 and name C7
> I am using version1.6-289
> Thanks.
> Jobi
> refinement.geometry_restraints.edits {
> bond {
> action = *add
> atom_selection_1 = chain S and resid 501 and name C7
> atom_selection_2 = chain A and resid 25 and name SG
> distance_ideal = 2.35
> sigma = 0.1
> slack = None
> }
> }
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