[phenixbb] autobuild omit map as Fo-Fc

Terwilliger, Thomas C terwilliger at lanl.gov
Wed Mar 7 15:24:27 PST 2012

Hi Ursula,

If everything goes right, you should find the file:


which is your omit map.

Let me know if that does not exist.
All the best,
Tom T

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Ursula Schulze-Gahmen [uschulze-gahmen at lbl.gov]
Sent: Wednesday, March 07, 2012 1:12 PM
To: PHENIX user mailing list
Subject: [phenixbb] autobuild omit map as Fo-Fc

I calculated an omit-map for my model using the following command inpt:

phenix.autobuild data=HKL2000+R.mtz model=ptefb_A4_refine_43.pdb omit_region_specification=omit_around_pdb omit_box_pdb_list=G_chain.pdb composite_omit_type=refine_omit maps_only=true

I would like to display a 2Fo-Fc and Fo-Fc map but I cannot find the

overall_best_refine_map_coeffs.mtz output file that should have these coefficients according to the manual. I only see the overall_best_denmod_map_coeffs.mtz file.

Can somebody tell how to best get to an omit Fo-Fc or 2Fo-Fc map?



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

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