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

Oleg Sobolev osobolev at lbl.gov
Wed Nov 30 09:47:00 PST 2016


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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