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@lanl.gov> wrote:
Hi Hari,
What is your space group? 狢 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. 蘯erhaps 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@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 戹ersion 0.61 for my building and map display using fft
>> inside of coot .
>>
>>
>> hari
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>>

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