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

Bernhard Rupp hofkristallamt at gmail.com
Mon Mar 1 09:36:56 PST 2021

Here is what I did:

Install phenix

make a batch command in your path (eg phx.bat) that executes the environment setup, eg. 

Open terminal, execute that batch (modify as you like), and there you go

Usage: phenix.refine [options] [reflection_file] [pdb_file] [parameter_file]

Best, BR

-----Original Message-----
From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> On Behalf Of Muriel Gelin
Sent: Monday, March 1, 2021 09:08
To: phenixbb at phenix-online.org
Subject: [phenixbb] executing Phenix in a python script on a Windows OS

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

but I don't think it answers my question.

Thank you in advance for your help!


Dr Muriel Gelin

Research Engineer
Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced Biology, Chemistry, Informatics Studio"

CNRS UMR 5048 - UM - INSERM U 1054
29 rue de Navacelles

Tel: (33) 04 67 41 77 12

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