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

Here is what I have: In a prompt: C:\Users\MG>C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat C:\Users\MG>phenix.refine Usage: phenix.refine [options] [reflection_file] [pdb_file] [parameter_file] -------------------------------------------------------------------------------- In python: source = subprocess.Popen(str(r"C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat"), stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)

...

...

phenix.refine Traceback (most recent call last):   File "<stdin>", line 1, in <module> NameError: name 'phenix' is not defined py phenix.refine   File "<stdin>", line 1     py phenix.refine        ^

-------------------------------------------------------------------------------- If somebody see what is the problem. I'm afraid I am stuck ... Thank you all. Muriel Le 02/03/2021 à 11:03, gelin a écrit :

Dear Bernhard,

Thank you for your answer.

Executing phenix_env.bat in Windows command prompt works well, since I can then execute phenix.refine in the prompt.

So I tried to add in my python script something like that: source = subprocess.Popen(my_path\phenix_env.bat, stdin=subprocess.PIPE, stdout=subprocess.PIPE,                               stderr=subprocess.PIPE) Unfortunately, it doesn't work. I suppose the prompt environment is not modified.

Do you know how to do that in my python script so that I can then execute something like: xtriage = subprocess.Popen(["phenix.xtriage", my_mtz, "parameters.reporting.log=" + "xtriage.log")],                                stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)

Thank you for you help.

Muriel

Le 2021-03-01 18:36, Bernhard Rupp a écrit :

...

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

-----Original Message----- From: [email protected] On Behalf Of Muriel Gelin Sent: Monday, March 1, 2021 09:08 To: [email protected] 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 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

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-- 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.