[phenixbb] executing Phenix in a python script on a Windows OS
hofkristallamt at gmail.com
Mon Mar 1 09:36:56 PST 2021
Here is what I did:
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]
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
Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced Biology, Chemistry, Informatics Studio"
CNRS UMR 5048 - UM - INSERM U 1054
29 rue de Navacelles
34090 MONTPELLIER Cedex - FRANCE
Tel: (33) 04 67 41 77 12
This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
phenixbb mailing list
phenixbb at phenix-online.org
Unsubscribe: phenixbb-leave at phenix-online.org
More information about the phenixbb