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 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 -- 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 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr 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.
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 -- This email has been checked for viruses by AVG. https://www.avg.com
Here is what I did:
Install phenix
make a batch command in your path (eg phx.bat) that executes the environment setup, eg.
C:\Phenix\phenix-installer-1.19-4092-intel-windows-x86_64\phenix_env.bat
Open terminal, execute that batch (modify as you like), and there you go
c:\data\Dropbox\Refinements\5okl>phenix.refine
Usage: phenix.refine [options] [reflection_file] [pdb_file] [parameter_file]
....
Best, BR
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participants (3)
-
Bernhard Rupp -
Muriel Gelin -
Robert Oeffner