[phenixbb] phenix.multi_crystal_average with twinned data

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Mar 11 11:43:45 PDT 2009

Hi Mary,

I have not tried the phenix multi-crystal averaging procedure with twinned
data, but here are some suggestions of how to proceed.

1. This routine does not do any refinement, only density modification. 
The density modification step does not know about twinning, so it will be
necessary (if your data are significantly twinned) to supply structure
factor files with detwinned data. I will check with Peter Zwart on
producing detwinned data in phenix; it may be necessary to do that with
other tools as normally phenix.refine uses the original data and does the
calculations internally.

2.  The models you supply are used to (a) identify NCS symmetry and
cross-crystal symmetry. Therefore it should not really matter if these
models are incomplete, and therefore the approach you are using should
work for improving the region where you have no model. The region where
NCS is applied is defined as a region centered near the center-of-mass of
the supplied model over which the NCS correlation is high.

I hope that helps!
All the best,
Tom T

I started running this function and then realized that I probably need to
do something to take the perfect twinning into account.  I'm not sure of
the best way to do this. I believe the map coefficients output by a run
phenix.refine should be detwinned as I give a twin law when running
phenix.refine.  Should I detwin the mtz containing the data and then use
those files for the multi crystal averaging?  Is there a way to output
detwinned data mtz files in phenix or do I need to use another program?

Also, I have two ncs copies in the ASU.  There's a region of density in
both ncs copies that I'm trying to improve the maps for with the multi
crystal averaging.  I don't have anything built in the region yet.  Is
there a way to use the NCS and multi crystal averaging at the same time
without any pdb coordinates in that region?

Even with my goof up about the twinning, the eff script I created
appeared to run without problems.


Mary X. Fitzgerald
Postdoctoral Associate
Arnold Lab
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