[phenixbb] coordinates and map shifted after phenix.refine without simulated annealing

hari jayaram harijay at gmail.com
Sat Jun 6 08:00:53 PDT 2009


I think I just understood your explanation for the shift after rigid body.
The rigid body phenix.refine picked an origin very close by in my P1 Cell ,
since the choice is arbitrary anyways . And so the output was off .
And I can see how an option to maintain centre of mass will solve that
problem
Thanks again

Hari


On Sat, Jun 6, 2009 at 10:51 AM, hari jayaram <harijay at gmail.com> wrote:

>
> Hello Tom ,
> Thanks for your speedy reply
>
> My space group is P1 , and the shift is by around an 1.2 A away and very
> much in the vicinity of the input model and experimental map
> I suspected the rigid body step (
> rigid_body+individual_sites+individual_adp+tls) might be causing this and so
> I am trying a refinement without the rigid body.
> Also I am quite close to convergence and that step should not be necessary
> as a first step.
>
> But I am still confused as to why it shifts the molecule very close by ,
> but slightly off , like a off kilter MR solution.
>
>
> Hari
>
>
>
> On Sat, Jun 6, 2009 at 10:40 AM, Thomas C. Terwilliger <
> terwilliger at lanl.gov> wrote:
>
>> Hi Hari,
>> What is your space group?  I am guessing that the shift is along an axis
>> where the origin is not fixed, for example the b axis in P21. This could
>> happen with rigid-body refinement where a molecule can move as a whole so
>> that the center of mass could move along that axis.  Perhaps someone else
>> can comment as to whether there is or could be an optional term in
>> phenix.refine to maintain the center of mass at the same coordinate in
>> such cases.
>> All the best,
>> Tom T
>>
>> >> Hi i am using phenix version 1.4 release tag 70
>> >>
>> >> hari at charlie:~$ phenix.refine --version
>> >>
>> -------------------------------------------------------------------------------
>> >>   PHENIX: Python-based Hierarchical ENvironment for Integrated
>> >> Xtallography
>> >>   Version: 1.4
>> >>   Release tag: 70
>> >>   Platform: intel-linux-2.6-x86_64 linux
>> >>   User: hari
>> >>
>> -------------------------------------------------------------------------------
>> >>
>> >>
>> >> I am seeing a strange shifting of my coordinates "out of my
>> experimental
>> >> phases map" before and after refinement without simulated annelaing
>> >>
>> >> I am at the final stages of my refinement. When I refine without
>> simulated
>> >> annealing the resulting model is shifted relative to my experimental
>> >> phases
>> >> map into which I build my model
>> >> The phenix command line strategy i am using are
>> >> rigid_body+individual_sites+individual_adp+tls .or the same strategy
>> with
>> >> simulated_annealing=true
>> >>
>> >> The output map coefficients fortunately match my model in both cases .
>> But
>> >> I
>> >> am wondering why there is a difference.
>> >> I am using the mlhl target for refinement to 3.1 A , My R and rfree is
>> >> 28/31
>> >> .
>> >>
>> >> Any ideas why my model shifts without simulated annealing . All pdbs
>> have
>> >> the same CRYST  record .
>> >> I am using coot  version 0.61 for my building and map display using fft
>> >> inside of coot .
>> >>
>> >>
>> >> hari
>> >> _______________________________________________
>> >> phenixbb mailing list
>> >> phenixbb at phenix-online.org
>> >> http://www.phenix-online.org/mailman/listinfo/phenixbb
>> >>
>>
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>
>
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