[phenixbb] completing the description of a residue according to idealized geometry
Nigel W Moriarty
NWMoriarty at lbl.gov
Wed Apr 14 09:01:33 PDT 2010
Peter
I believe that something could be done in this regard. I'd be
interested in taking a look if you could send the files directly to me
in the strictest confidence. Of course, the answer is to use Coot but
for 200 cobalts that is a lot of work. I'll try to write a script that
will add them all automatically.
Nigel
On 4/14/10 8:37 AM, Peter Grey wrote:
> 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
> <mailto: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
> > _______________________________________________
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> > phenixbb at phenix-online.org <mailto: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 <mailto:rjr27 at cam.ac.uk>
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk <http://www-structmed.cimr.cam.ac.uk>
>
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>
>
>
>
> --
> Peter
> ------------------------------------------------------------------------
>
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--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
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