[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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