[phenixbb] how to fix a side chain not to be refined?

Nathaniel Echols nechols at lbl.gov
Fri Apr 19 14:20:21 PDT 2013

On Fri, Apr 19, 2013 at 2:14 PM, Rongjin <guanrj at foxmail.com> wrote:
> I have an Arg with flexible side chain, close to an iodide ion. Every time
> I refine it, the side chain of Arg will push the iodide ion away, even I
> selected

The syntax below looks correct to me, although you should probably do
the same thing for the ADP selection, but it's a little disturbing
that it's doing this.  Do you have rotamer correction turned on?  That
may be the problem, if it is trying to fit to the difference density
(I don't think it's very aware of nearby atoms).


> the Arg not to be refined:
>   refine {
>     strategy = *individual_sites individual_sites_real_space rigid_body \
>                *individual_adp group_adp  tls  *occupancies group_anomalous
>      sites {
>            individual = "not (chain A and resid 40)"
>            }
>          }
> The residue 40 in Chain A is that Arg close to the Iodide. Is this selection
> correct?
> How to fix the side chain of Arg in refinement?
> I attached two pictures, one before and one after refinement, the local area
> of the Arg
> and the iodide. The iodide is bound to an Asn residue of one symmetric
> molecule.
> Thank you
> Rongjin Guan
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