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

[Peter Grey]

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 <NWMoriarty at lbl.gov>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 <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
>> > 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
>> Cambridge CB2 0XY, U.K.
>> 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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>


-- 
Peter
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