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

Tim Gruene tim.gruene at psi.ch
Wed Nov 30 00:16:49 PST 2016

Hi Andrew,

in case you are familiar with scripting, you can use code like

my_d_min=$(mtzdmp  lys2_final.mtz  | grep -A2 "Resolution Range" | tail -n1 | 
awk '{print $6 }')

(all in one line) and use the command line calculator 'bc' to increase 
my_d_min in a loop.

As a remark, I would use equal volumes rather than equal distances, as the 
number of reflections is linear to the volume of the Ewald sphere, not linear 
to the resolution.


On Tuesday, November 29, 2016 05:21:56 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
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297


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