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

Edward A. Berry BerryE at upstate.edu
Wed Nov 30 09:34:56 PST 2016

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)
If not, do command line parameters override what is in the eff file? Like:

foreach HIRES ( 2.5 2.4 2.3 2.2 )
phenix.refine refine.eff refinement.xray_data.high_resolution=$HIRES refinement.output.prefix=ref${HIRES}

where the shell (tcsh) would substitute the variables before submitting to phenix?

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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