Hi,


I am the developer of the PyChimera wrapper! Glad to know someone besides me is actually trying to use it!


If you installed pychimera with pip or conda, you should have an executable called 'pychimera'. With it you can run the script directly with pychimera, like 'pychimera myscript.py'. Also, a bare PyChimera command ('pychimera') should bring up a Python interpreter where you can do "import chimera" just fine.


Let me know if you are able to make it work!


Jaime Rodríguez-Guerra Pedregal
Molecular modeling of transition metal systems group
Department of Chemistry, Faculty of Sciences
Universitat Autňnoma de Barcelona

Edif. C ˇ C7/153
Campus de la UAB ˇ 08193 Bellaterra
(Cerdanyola del Vallčs) ˇ Barcelona ˇ Spain

+34 93 581 28 57
www.uab.cat

  

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De: chimera-users-bounces@cgl.ucsf.edu <chimera-users-bounces@cgl.ucsf.edu> en nombre de chimera-users-request@cgl.ucsf.edu <chimera-users-request@cgl.ucsf.edu>
Enviado: martes, 21 de junio de 2016 21:00:02
Para: chimera-users@cgl.ucsf.edu
Asunto: Chimera-users Digest, Vol 158, Issue 30
 
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Today's Topics:

   1. Re: Module import error (Subha Kalyaanamoorthy)
   2. Re: Module import error (Greg Couch)


----------------------------------------------------------------------

Message: 1
Date: Mon, 20 Jun 2016 16:27:14 -0600
From: Subha Kalyaanamoorthy <kalyaana@ualberta.ca>
To: Chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Module import error
Message-ID:
        <CAFuN1V=PtjK=nBd6+-_4Tir1T+xc8JebJvx0frzbeoyqEUq1og@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Greg,

Thanks for the kind reply.
Sorry about the typo.

The environment variables of the system seem fine to me. I also tried
calling Chimera  from the same directory as the script and its working
fine.

However, calling the chimera script using "python sample.py" doesn't work
and using absolute path to chimera didn't help too.

I tried installing pychimera, but end up with the same kind of error when I
try pychimera -i
import pychimera

ImportError: No module named pychimera


Couldn't understand what's going on with these import modules.


I would greatly appreciate any suggestions to solve this.


Thanks,

Subha

On Mon, Jun 20, 2016 at 4:05 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:

> (I assume you meant --nostatus)
>
> For me the simple test of a file with:
>
> import os
> os.system("chimera --nogui --nostatus")
>
> works just fine.  So it's probably something about your particular setup
> that is tickling this bug.
>
> It might be the directory that you're running the script in, it might have
> python modules/packages that conflict with chimera's.  Or it might
> something in the environment.  Chimera tries to protect its python from the
> user's environment, but maybe we missed something.  Also double check that
> the chimera you're invoking is the one you're expecting -- try using an
> absolute path to chimera while you're debugging this.
>
>     HTH,
>
>     Greg
>
>
> On 06/20/2016 01:18 PM, Subha Kalyaanamoorthy wrote:
>
> Hi There,
>
> I am trying to call a script with Chimera commands(saved as sample.py
> file)  in another python program using os.system("chimera --nogui --nostats
> sample.py") and I get an module load error as below,
>
> import chimera
>
> ImportError: No module named chimera
>
>
> However, if I call the script with chimera it works, for eg., chimera
> --nogui --nostats sample.py typed directly in terminal is working.
>
>
> Can anybody help fix this error?
>
>
> Thanks in advance,
>
> Best Regards,
>
> Subha
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>


--
Dr. Subha Kalyaanamoorthy
Post Doctoral Fellow
Faculty of Pharmacy and Pharmaceutical Sciences
University of Alberta
Edmonton, Canada.
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Message: 2
Date: Mon, 20 Jun 2016 15:50:38 -0700
From: Greg Couch <gregc@cgl.ucsf.edu>
To: Subha Kalyaanamoorthy <kalyaana@ualberta.ca>,
        Chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Module import error
Message-ID: <5768733E.3060209@cgl.ucsf.edu>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"

Change your os.system("chimera ...") to os.system("env PYTHONVERBOSE=1
chimera ...") and the debugging output might give you a clue.  Feel free
to send me the voluminous output (and just me, not the whole
chimera-users list), and I'll let you know if I spot anything.

     -- Greg

On 06/20/2016 03:27 PM, Subha Kalyaanamoorthy wrote:
> Hi Greg,
>
> Thanks for the kind reply.
> Sorry about the typo.
>
> The environment variables of the system seem fine to me. I also tried
> calling Chimera  from the same directory as the script and its working
> fine.
>
> However, calling the chimera script using "python sample.py" doesn't
> work and using absolute path to chimera didn't help too.
>
> I tried installing pychimera, but end up with the same kind of error
> when I try pychimera -i
> import pychimera
>
> ImportError: No module named pychimera
>
>
> Couldn't understand what's going on with these import modules.
>
>
> I would greatly appreciate any suggestions to solve this.
>
>
> Thanks,
>
> Subha
>
>
> On Mon, Jun 20, 2016 at 4:05 PM, Greg Couch <gregc@cgl.ucsf.edu
> <mailto:gregc@cgl.ucsf.edu>> wrote:
>
>     (I assume you meant --nostatus)
>
>     For me the simple test of a file with:
>>     import os
>>     os.system("chimera --nogui --nostatus")
>     works just fine.  So it's probably something about your particular
>     setup that is tickling this bug.
>
>     It might be the directory that you're running the script in, it
>     might have python modules/packages that conflict with chimera's.
>     Or it might something in the environment.  Chimera tries to
>     protect its python from the user's environment, but maybe we
>     missed something.  Also double check that the chimera you're
>     invoking is the one you're expecting -- try using an absolute path
>     to chimera while you're debugging this.
>
>         HTH,
>
>         Greg
>
>
>     On 06/20/2016 01:18 PM, Subha Kalyaanamoorthy wrote:
>>     Hi There,
>>
>>     I am trying to call a script with Chimera commands(saved as
>>     sample.py file)  in another python program using
>>     os.system("chimera --nogui --nostats sample.py") and I get an
>>     module load error as below,
>>
>>     import chimera
>>
>>     ImportError: No module named chimera
>>
>>
>>     However, if I call the script with chimera it works, for eg.,
>>     chimera --nogui --nostats sample.py typed directly in terminal is
>>     working.
>>
>>
>>     Can anybody help fix this error?
>>
>>
>>     Thanks in advance,
>>
>>     Best Regards,
>>
>>     Subha
>>
>>
>>
>>
>>     _______________________________________________
>>     Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu>
>>     Manage subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>
> --
> Dr. Subha Kalyaanamoorthy
> Post Doctoral Fellow
> Faculty of Pharmacy and Pharmaceutical Sciences
> University of Alberta
> Edmonton, Canada.
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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