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@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
------
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@cam.ac.uk
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
--
Peter
--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov