[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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>
>     ------
>     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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