[phenixbb] ncs_average output map

Tom Terwilliger terwilliger at lanl.gov
Mon Dec 12 11:35:33 PST 2011

Hi Ursula,

I am not sure if this is the (only) problem, but phenix.ncs_average does not know about NCS groups, so it only takes the first NCS group and averages it and writes out the map where that group has been averaged. 

So supposedly phenix.ncs_average should (1) average the density in the region where the 1st NCS group applies, and (2) leave original density elsewhere.

Is that consistent with what you see?

All the best,
Tom T

On Dec 12, 2011, at 12:27 PM, Ursula Schulze-Gahmen wrote:

> I am puzzled about my ncs-averaged output map. 
> I determined the ncs relation using phenix.find_ncs with pdb and mtz input. The program finds 2 NCS groups with 3 molecules each and the rmsds are low. I then read in the ncs_spec file and an mtz file with map coefficients into phenix.ncs_average. I used the FOFCWT, PHFOFCWT coefficients. The output map seems cleaner than the unaveraged map and shows some of the same features, but the density around the 3 molecules is not identical. 2 of them look very similar, but the density around one of them is somewhat different. How is this possible if the map is averaged?
> Thanks for any suggestions or explanations.
> Ursula
> -- 
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

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