[phenixbb] completing the description of a residue according to idealized geometry

[Peter Grey]

Dear Randy,

I apologize for so badly presenting my case. I was referring  to the first
option, i.e. completing these components (200 cobalt hexamine sites) in the
whole structure file.

Peter.


On Wed, Apr 14, 2010 at 3:12 PM, Randy Read <rjr27 at cam.ac.uk> wrote:

> Dear Peter,
>
> It's not clear to me whether you want to complete the cobalt hexamine
> structures to improve the substructure model and thus the phases, or you
> have a protein model and just want to complete this component of the whole
> structure.  I'll assume it's the former.
>
> At the moment, you can't do this in Phaser (which is doing the SAD phasing
> part), though allowing rigid-body clusters is on our long-term wish list.
>  However, I don't think you'll gain much in phasing power by modelling the
> amine groups, as they're not particularly heavy and have no significant
> anomalous scattering.  If you can see the amine groups in the density maps
> (which you would need to be able to do to model them), then presumably you
> can also see elements of secondary structure.  My gut feeling is that you'd
> get more improvement in the maps from carrying out iterative model building
> and density modification.
>
> Regards,
>
> Randy Read
>
> On 14 Apr 2010, at 13:18, Peter Grey wrote:
>
> > Dear Phenix users,
> >
> > My crystals contains many copies of cobalt hexamine (used for SAD
> phasing). Currently the model contains only the cobalt ions (without the
> amines)  and I am looking for a tool that will use the idealized geometry of
> cobalt hexamine to complete the description of these resdiues, i.e. add ATOM
> lines for the amines
> >
> > Is there such a tool ?
> >
> > Hoping,
> >
> > Peter
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
>
> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research      Tel: + 44 1223 336500
> Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
> Hills Road                                    E-mail: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk
>
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>



-- 
Peter
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