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

[Muriel Gelin]

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: 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
>> 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


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