[phenixbb] Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density

Pavel Afonine pafonine at lbl.gov
Wed Nov 30 09:52:06 PST 2016


As an update: I wrote a Python script that hopefully does what Andrew 
wanted. The script does not use command line tools (like 
phenix.something) but instead it is using CCTBX functions directly (90 
lines of Python code).

Pavel

On 11/30/16 09:47, Oleg Sobolev wrote:
> Hi Edward,
>
>     I had a related question- is it possible to have env. variables
>     evaluated in an eff file?
>     (Like in cns, {===>}
>     parameter_infile_1="CNS_TOPPAR:protein_rep.param";, CNS_TOPPAR is
>     env var)
>
> I'm afraid no.
>
>     If not, do command line parameters override what is in the eff
>     file? Like:
>
> Yes, whatever is in command-line arguments overrides values in .eff file.
> I think simple bash/tsch script would be the easiest way to solve the 
> original Andrew's problem.
>
> Best regards,
> Oleg Sobolev.
>
>
>
>     On 11/29/2016 05:21 PM, Andrew Morin wrote:
>
>         Hello,
>
>         I am trying to find a convenient way to generate maps using
>         phenix.mtz2map at increasingly greater values of d_min.
>
>         For example:
>
>         I have a .mtz file of a structure solved at 2.4A. I run
>         phenix.mtz2map with d_min=none and obtain a map using all of
>         the resolution data. I would like to also create 10 more maps
>         with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A.
>         An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc.
>
>         Might anyone know of a handy way to automate this over a large
>         number of mtz files?
>
>         ALTERNATIVELY - I am performing a phenix.cut_out_density step
>         prior to this. So if it might be easier to automate a
>         incrementing high resolution cutoff in phenix.cut_out_density,
>         that would also work.
>
>         Thanks for your help.
>
>         -Andrew
>
>
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