[phenixbb] omit map with twinning?

Nathaniel Echols NEchols at lbl.gov
Wed Feb 17 14:08:28 PST 2010

On Feb 17, 2010, at 1:46 PM, Kelly Daughtry wrote:
> The omit_map in the new gui (version 1.5) is great, but I can not
> include a twin law when calculating the omit map, thus the result is
> very messy unclear maps. I do not know if 1.6 has the solution or not,
> I am still lobbying our computer guy to upgrade to it...
> Is there a way from the command line i can include the twin law in
> autobuild so I can calculate the omit map, or can I just add it into
> the eff file?

In theory, yes: create a configuration file "refinement.eff", with this content:

refinement.twinning.twin_law = "X"

(where X is the desired twin law)

In the GUI, you can add this file like any other, and it should recognize it as a config file.  You'll need to change the type to "Refine config", which specifies that it will be passed to phenix.refine.  (You may see an error message when you modify that control - in 1.6, at least - but it should still change the file type.)  On the command line, autobuild.input_files.refine_eff_file_list=refinement.eff should do the equivalent.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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