Hi i am using phenix version 1.4 release tag 70<br><br>hari@charlie:~$ phenix.refine --version<br>-------------------------------------------------------------------------------<br>  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography<br>
  Version: 1.4<br>  Release tag: 70<br>  Platform: intel-linux-2.6-x86_64 linux<br>  User: hari<br>-------------------------------------------------------------------------------<br><br><br>I am seeing a strange shifting of my coordinates &quot;out of my experimental phases map&quot; before and after refinement without simulated annelaing<br>
<br>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<br>The phenix command line strategy i am using are rigid_body+individual_sites+individual_adp+tls .or the same strategy with simulated_annealing=true <br>
<br>The output map coefficients fortunately match my model in both cases . But I am wondering why there is a difference.<br>I am using the mlhl target for refinement to 3.1 A , My R and rfree is 28/31 .<br><br>Any ideas why my model shifts without simulated annealing . All pdbs have the same CRYST  record .<br>
I am using coot  version 0.61 for my building and map display using fft inside of coot .<br><br><br>hari<br><br>