[phenixbb] Help with custom bond restraints syntax

Jeff Headd jjheadd at lbl.gov
Thu Oct 21 06:33:30 PDT 2010


Hi Jobi,

Your selection syntax looks correct to me.  Would you be willing to
send me your coordinates and data (directly to me, not to the list) so
that I can have a closer look at what is going on?

The version of PHENIX you are using is also quite old, so I would
recommend upgrading to a more recent installer.

Thanks,
Jeff

On Thu, Oct 21, 2010 at 1:49 AM, Jobichen Chacko <jobichenc at gmail.com> 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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>



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