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

Randy Read rjr27 at cam.ac.uk
Wed Apr 14 06:12:08 PDT 2010

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.


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
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