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

Pavel Afonine pafonine at lbl.gov
Fri Apr 19 14:25:41 PDT 2013


Hi Rongjin,

could you please send me the data and model files? I'm very interested 
to see what's happening and why.

Thanks,
Pavel

On 4/19/13 2:14 PM, Rongjin wrote:
> Hello
>
> 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 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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