[phenixbb] coordinates and map shifted after phenix.refine withoutsimulated annealing

Mirek Cygler mirek at bri.nrc.ca
Sat Jun 6 11:39:24 PDT 2009

Dear Joel,
    I received your previous email with the ms. Will repy in a few days.


From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org] 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 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

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 .


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