[phenixbb] Can phenix generate the NCS masks just like CCP4-NCSMASK does?

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Apr 13 19:44:59 PDT 2011

Hi Hailiang,

Yes, you can run phenix.autobuild with your data file, sequence file,
model (if any), maps_only=True and ncs_output_mask_file=my_mask_file.map 
and ncs_file=my_ncs.ncs_spec and it should write out a ccp4-style
my_mask_file.map file showing the ncs asymmetric unit (in addition to
generating map coefficients for a density-modified map).

The my_mask_file.map will be in AutoBuild_run_1_/TEMP0/

I used these commands just now to test it out (takes about 10 minutes; you
can do the same if you want because the data for the regression tests are
in your phenix installation already):

phenix_regression.wizards.test_command_line_ncs test_find_ncs_from_density
cd test_find_ncs_from_density/
phenix.autobuild maps_only=true ncs_file= find_ncs.ncs_spec \
   data= cycle_best_1.mtz seq_file= sequence.dat \

(The first two commands are just to set up some data that has NCS in it
and to find that NCS; in this case 6 NCS copies. You presumably already
have done both of these already and so you can go right to the autobuild
maps_only step.)

Looking at my_mask_file.map and resolve_work.mtz in the resulting
AutoBuild_run_1_/TEMP0/ directory, you can see that one asymmetric unit of
the NCS is within region defined by the my_mask_file.map.

I hope that helps!
-Tom T

> Hi there,
>> Can phenix generate the NCS masks just like CCP4-NCSMASK does?
>> Thanks!
>> Hailiang
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb

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