[phenixbb] Help with custom bond restraints syntax

Pavel Afonine PAfonine at lbl.gov
Tue Sep 29 09:21:30 PDT 2009


Alternatively, you can do simply this:

refinement.geometry_restraints.edits {
   bond {
        action = *add
        atom_selection_1 = chain F and resid 1 and name FE1
        atom_selection_2 = chain A and resid 69 and name SG
        distance_ideal = 2.35
        sigma = 0.1
        slack = None
   }
}


Pavel.


On 9/29/09 8:54 AM, Andrew T. Torelli wrote:
> Hi all,
>
>      I'm having what I believe is a simple problem defining custom bond
> restraints between a side chain in my protein model and a ligand
> (non-covalent bond).  Here is a minimal form of my custom bond
> definition file that suffers from the error:
>
> refinement.geometry_restraints.edits {
>    Atom1  = chain F and resid 1 and name FE1
>    Atom2  = chain A and resid 69 and name SG
>    bond {
>         action = *add
>         atom_selection_1 = Atom1
>         atom_selection_2 = Atom2
>         distance_ideal = 2.35
>         sigma = 0.1
>         slack = None
>    }
> }
>
>      I'm using phenix 1.4-153 and I get the following error:
> ERROR: Unused parameter definitions:
>   refinement.geometry_restraints.edits.Atom1 (file
> "/HOME/andrew/PHENIX_paramfiles/test.edits", line 5)
>   refinement.geometry_restraints.edits.Atom2 (file
> "/HOME/andrew/PHENIX_paramfiles/test.edits", line 6)
>
>      I've checked through the online manual and I believe my syntax is
> correct, but I'm not sure why my custom bond restraint is being
> ignored.
>
>      A second question is: once I get the custom bond/angle restraints
> correctly implemented, is there a better or more convenient place to
> look and confirm that the restraints have been imposed other than the
> .geo file phenix.refine outputs?
>
> Thank you very much for your help,
> -Andy
>
>
>
>
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