[Chimera-users] Chimera-users Digest, Vol 158, Issue 30

Jaime Rodríguez-Guerra Pedregal Jaime.RodriguezGuerra at uab.cat
Tue Jun 21 12:37:33 PDT 2016


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 Autònoma de Barcelona

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

+34 93 581 28 57
www.uab.cat<http://www.uab.cat/>

 [http://www.uab.cat/vcard/Logo_ORCID_0.png] <http://orcid.org/0000-0001-8974-1566>  [http://www.uab.cat/vcard/Logo_LinkedIn_0.png] <https://www.linkedin.com/in/jaimergp>

This message may contain private or confidential information, and is addressed exclusively to its intended recipient. If you have received it in error, please notify the sender and delete it. Please bear in mind that you are not authorized to use it for any purposes.

Please consider the environment before printing this email.

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

Send Chimera-users mailing list submissions to
        chimera-users at cgl.ucsf.edu

To subscribe or unsubscribe via the World Wide Web, visit
        http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
or, via email, send a message with subject or body 'help' to
        chimera-users-request at cgl.ucsf.edu

You can reach the person managing the list at
        chimera-users-owner at cgl.ucsf.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Chimera-users digest..."


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 at ualberta.ca>
To: Chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Module import error
Message-ID:
        <CAFuN1V=PtjK=nBd6+-_4Tir1T+xc8JebJvx0frzbeoyqEUq1og at 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 at 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 at 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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160620/aca3a7da/attachment-0001.html>

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

Message: 2
Date: Mon, 20 Jun 2016 15:50:38 -0700
From: Greg Couch <gregc at cgl.ucsf.edu>
To: Subha Kalyaanamoorthy <kalyaana at ualberta.ca>,
        Chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Module import error
Message-ID: <5768733E.3060209 at 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 at cgl.ucsf.edu
> <mailto:gregc at 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 at cgl.ucsf.edu <mailto:Chimera-users at 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 at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160620/ffd8fb26/attachment-0001.html>

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

_______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


End of Chimera-users Digest, Vol 158, Issue 30
**********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160621/382d94f1/attachment-0001.html>


More information about the Chimera-users mailing list