[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
myscript.py.
Alternatively, locate the installation path of Phenix on your PC, say
C:\Users\Oeffner\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64.
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.
Rob
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
www.cimr.cam.ac.uk/investigators/read/index.html
tel: +44(0)1223 763234
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