[phenixbb] executing Phenix in a python script on a Windows OS

Robert Oeffner rdo20 at cam.ac.uk
Mon Mar 1 09:35:19 PST 2021

Dear Muriel,

If you installed Phenix on a Windows PC under the start menu you'll find 
a Phenix folder. Besides the Phenix icon for launching the GUI it also 
contains a link to a command prompt with the Phenix environment already 
loaded. You can run your scripts from there by calling phenix.python 

Alternatively, locate the installation path of Phenix on your PC, say 
It contains a file named phenix_env.bat that you can call in any command 
prompt to set up the phenix environment.

Feel free to get in touch if you have more questions.


On 01-03-2021 17:07, Muriel Gelin wrote:
> Dear Phenix community,
> I wrote a python script to automate the processing of our data with 
> Phenix. I'm not a developer by profession, but a crystallographer, and 
> write scripts usually under Linux. My colleagues working under Windows 
> asked me to share my script.
> I managed to run a simple python script under windows, no problem. But 
> for a script that executes Phenix, it's not so easy (for me).
> Under Linux, I manage to source phenix_env.csh, but under Windows what 
> is the command to setup Phenix  in order to simply use phenix.refine 
> or phenix.xtriage in my script?
> All I can find is this page 
> https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/phenix/install-setup-run.html
> but I don't think it answers my question.
> Thank you in advance for your help!
> Muriel
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
The Keith Peters Building
Hills Road
Cambridge CB2 0XY
tel: +44(0)1223 763234

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