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).

Pavel.

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

}

}