[phenixbb] Structure with pseudo-NCS translation

Esko Oksanen esko.oksanen at esss.se
Fri Apr 3 09:01:41 PDT 2015

 Hi Mark,

I believe at least part of the problem arises already in the scaling stage, where the programs assume a unimodal distribution which is not the case in the presence of pseudo-translations. We encountered a similar issue with refinement and pseudo-translation, where I simply scaled the systematically weak data separately from the strong and did rigid body refinement against the weak data and restrained against the strong. The details can be found in http://scripts.iucr.org/cgi-bin/paper?ea5052.


Esko Oksanen, PhD
Instrument Scientist - Neutron Macromolecular Crystallography

European Spallation Source ESS AB
P.O Box 176, SE-221 00 Lund, Sweden
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E-mail: esko.oksanen at esss.se<mailto:esko.oksanen at esss.se>


On 03 Apr 2015, at 15:59, Mark A Saper <saper at umich.edu<mailto:saper at umich.edu>> wrote:

I know that Phaser takes account of NCS translation in the likelihood statistics ( Read, Adams, McCoy (2013) Intensity statistics in the presence of translational non crystallographic symmetry”). Has this also been incorporated into phenix.refine?  I have a structure with pseudo NCS translations because of NCS rotational symmetry. One suggestion that I found in the archives, was to explicitly LS target refinement rather than ML.  Any comments?

Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, University of Michigan
Ann Arbor MI  48109-1055 U.S.A.
saper at umich.edu<mailto:saper at umich.edu>     phone (734) 764-3353     fax (734) 764-3323

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