Probably my fault - I interpreted it correctly at first but then started to wonder whether I might be misunderstanding! Can you see the amine groups in the density? That's an awful lot of sites in the substructure, so presumably it's a very large structure. If not, then I suppose the amines could contribute a meaningful amount to model the total scattering. Regards, Randy On 14 Apr 2010, at 16:37, 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 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 [email protected] 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Peter _______________________________________________ phenixbb mailing list [email protected] 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

Hi Nigel, Thank you very much for agreeing to help and for the idea of using Coot. I think I can write a small script that will use Coot powers to change it automatically for all these residues. Thank you again for helping, Peter. On Wed, Apr 14, 2010 at 6:01 PM, Nigel W Moriarty wrote:

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 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 [email protected] 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Peter

------------------------------

_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Peter