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

Pavel Afonine pafonine at lbl.gov
Fri Apr 19 21:11:11 PDT 2013


Yep, this is not too surprising since the current phenix.refine 
implementation of rotamer fitting does not use the new residue/rotamer 
fitting machinery (the one I showed at past WCPCW), which will be in 
place in a few coming months. Stay tuned!

Pavel

On 4/19/13 7:27 PM, Rongjin wrote:
> Hi Nat,
>
> You are right. By turning off the "fix rotamers" the Arg does not move 
> any more.
>
> Best
>
> Rongjin
>
>
> ------------------ Original ------------------
> *From: * "Nathaniel Echols"<nechols at lbl.gov>;
> *Date: * Apr 20, 2013
> *To: * "PHENIX user mailing list"<phenixbb at phenix-online.org>;
> *Subject: * Re: [phenixbb] how to fix a side chain not to be refined?
>
> 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).
>
> -Nat
>
> > 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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> >
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