It depends what the purpose of your averaging is...that routine is mainly designed to quickly show you what your averaged map would look like. If you are doing density modification then you can use

phenix.autobuild \

ncs_file=myncs.ncs_spec \

data=datafile.mtz \

input_map_file=working_map_coeffs.mtz \

seq_file = seq.dat \

maps_only=True

and that should run ncs averaging using both NCS groups. Let me know if that doesn't do what it is supposed to!

All the best,

Tom T

On Dec 12, 2011, at 12:44 PM, Ursula Schulze-Gahmen wrote:

That could be right. Would you suggest to do the averaging in CCP4 instead?

Ursula

On Mon, Dec 12, 2011 at 11:35 AM, Tom Terwilliger <[email protected]> wrote:

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
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Los Alamos National Laboratory
Los Alamos, NM 87545

Tel: 505-667-0072 email: [email protected]
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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--
Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220

_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel: 505-667-0072 email: [email protected]
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss