Alternatively - why not script it together in a command file from a Windows terminal? For many basic tasks this works fine (not necessarily elegant) & you can mix ccp4 and phenix as you like? Best, BR -----Original Message----- From: [email protected] On Behalf Of Robert Oeffner Sent: Tuesday, March 2, 2021 11:21 To: [email protected] Subject: Re: [phenixbb] executing Phenix in a python script on a Windows OS Dear Muriel, The file C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat should not be run from a python subprocess. It is only used once for initialising the pheinix environment in your command prompt so that you may start phenix.python, phenix.refine or any other phenix.some_command from there. Once you have started a phenix.python session from a command prompt you then need to import various modules such as the phenix, iotbx, cctbx, etc in order to use functions available from these. If you're not used to write and work with python scripts it's not productive use of time to write python scripts for phenix.refine. It may be easier to do what you want just using the command line interface of phenix.refine. Regards, Robert On 02-03-2021 16:36, Muriel Gelin wrote:

Here is what I have:

In a prompt:

C:\Users\MG>C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-wind ows-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-r un.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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