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From: [email protected] [mailto:[email protected]] On Behalf Of hari jayaram
Sent: Saturday, June 06, 2009 10:02 AM
To: PHENIX user mailing list
Subject: [phenixbb] coordinates and map shifted after phenix.refine withoutsimulated annealing

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  version 0.61 for my building and map display using fft inside of coot .


hari