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

[zhangh1 at umbc.edu]

Got it!

> 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 \
>    ncs_output_mask_file=my_mask_file.map
>
> (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
>>>
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