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<p>Hi,</p>
<p><br>
</p>
<p>I am the developer of the PyChimera wrapper! Glad to know someone besides me is actually trying to use it!</p>
<p><br>
</p>
<p>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.</p>
<p><br>
</p>
<p>Let me know if you are able to make it work!</p>
<p><br>
</p>
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<span style="font-size:8pt"><span style=""><span style="color:rgb(165,75,4); font-weight:bold">Jaime Rodríguez-Guerra Pedregal</span><br style="">
<b style="">Molecular modeling of transition metal systems group</b></span><br style="">
Department of Chemistry, Faculty of Sciences</span></div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De:</b> 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><br>
<b>Enviado:</b> martes, 21 de junio de 2016 21:00:02<br>
<b>Para:</b> chimera-users@cgl.ucsf.edu<br>
<b>Asunto:</b> Chimera-users Digest, Vol 158, Issue 30</font>
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Today's Topics:<br>
<br>
1. Re: Module import error (Subha Kalyaanamoorthy)<br>
2. Re: Module import error (Greg Couch)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 20 Jun 2016 16:27:14 -0600<br>
From: Subha Kalyaanamoorthy <kalyaana@ualberta.ca><br>
To: Chimera-users@cgl.ucsf.edu<br>
Subject: Re: [Chimera-users] Module import error<br>
Message-ID:<br>
<CAFuN1V=PtjK=nBd6+-_4Tir1T+xc8JebJvx0frzbeoyqEUq1og@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Greg,<br>
<br>
Thanks for the kind reply.<br>
Sorry about the typo.<br>
<br>
The environment variables of the system seem fine to me. I also tried<br>
calling Chimera from the same directory as the script and its working<br>
fine.<br>
<br>
However, calling the chimera script using "python sample.py" doesn't work<br>
and using absolute path to chimera didn't help too.<br>
<br>
I tried installing pychimera, but end up with the same kind of error when I<br>
try pychimera -i<br>
import pychimera<br>
<br>
ImportError: No module named pychimera<br>
<br>
<br>
Couldn't understand what's going on with these import modules.<br>
<br>
<br>
I would greatly appreciate any suggestions to solve this.<br>
<br>
<br>
Thanks,<br>
<br>
Subha<br>
<br>
On Mon, Jun 20, 2016 at 4:05 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:<br>
<br>
> (I assume you meant --nostatus)<br>
><br>
> For me the simple test of a file with:<br>
><br>
> import os<br>
> os.system("chimera --nogui --nostatus")<br>
><br>
> works just fine. So it's probably something about your particular setup<br>
> that is tickling this bug.<br>
><br>
> It might be the directory that you're running the script in, it might have<br>
> python modules/packages that conflict with chimera's. Or it might<br>
> something in the environment. Chimera tries to protect its python from the<br>
> user's environment, but maybe we missed something. Also double check that<br>
> the chimera you're invoking is the one you're expecting -- try using an<br>
> absolute path to chimera while you're debugging this.<br>
><br>
> HTH,<br>
><br>
> Greg<br>
><br>
><br>
> On 06/20/2016 01:18 PM, Subha Kalyaanamoorthy wrote:<br>
><br>
> Hi There,<br>
><br>
> I am trying to call a script with Chimera commands(saved as sample.py<br>
> file) in another python program using os.system("chimera --nogui --nostats<br>
> sample.py") and I get an module load error as below,<br>
><br>
> import chimera<br>
><br>
> ImportError: No module named chimera<br>
><br>
><br>
> However, if I call the script with chimera it works, for eg., chimera<br>
> --nogui --nostats sample.py typed directly in terminal is working.<br>
><br>
><br>
> Can anybody help fix this error?<br>
><br>
><br>
> Thanks in advance,<br>
><br>
> Best Regards,<br>
><br>
> Subha<br>
><br>
><br>
><br>
> _______________________________________________<br>
> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<br>
> Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
><br>
><br>
><br>
<br>
<br>
-- <br>
Dr. Subha Kalyaanamoorthy<br>
Post Doctoral Fellow<br>
Faculty of Pharmacy and Pharmaceutical Sciences<br>
University of Alberta<br>
Edmonton, Canada.<br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 20 Jun 2016 15:50:38 -0700<br>
From: Greg Couch <gregc@cgl.ucsf.edu><br>
To: Subha Kalyaanamoorthy <kalyaana@ualberta.ca>,<br>
Chimera-users@cgl.ucsf.edu<br>
Subject: Re: [Chimera-users] Module import error<br>
Message-ID: <5768733E.3060209@cgl.ucsf.edu><br>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
<br>
Change your os.system("chimera ...") to os.system("env PYTHONVERBOSE=1 <br>
chimera ...") and the debugging output might give you a clue. Feel free <br>
to send me the voluminous output (and just me, not the whole <br>
chimera-users list), and I'll let you know if I spot anything.<br>
<br>
-- Greg<br>
<br>
On 06/20/2016 03:27 PM, Subha Kalyaanamoorthy wrote:<br>
> Hi Greg,<br>
><br>
> Thanks for the kind reply.<br>
> Sorry about the typo.<br>
><br>
> The environment variables of the system seem fine to me. I also tried <br>
> calling Chimera from the same directory as the script and its working <br>
> fine.<br>
><br>
> However, calling the chimera script using "python sample.py" doesn't <br>
> work and using absolute path to chimera didn't help too.<br>
><br>
> I tried installing pychimera, but end up with the same kind of error <br>
> when I try pychimera -i<br>
> import pychimera<br>
><br>
> ImportError: No module named pychimera<br>
><br>
><br>
> Couldn't understand what's going on with these import modules.<br>
><br>
><br>
> I would greatly appreciate any suggestions to solve this.<br>
><br>
><br>
> Thanks,<br>
><br>
> Subha<br>
><br>
><br>
> On Mon, Jun 20, 2016 at 4:05 PM, Greg Couch <gregc@cgl.ucsf.edu <br>
> <<a href="mailto:gregc@cgl.ucsf.edu">mailto:gregc@cgl.ucsf.edu</a>>> wrote:<br>
><br>
> (I assume you meant --nostatus)<br>
><br>
> For me the simple test of a file with:<br>
>> import os<br>
>> os.system("chimera --nogui --nostatus")<br>
> works just fine. So it's probably something about your particular<br>
> setup that is tickling this bug.<br>
><br>
> It might be the directory that you're running the script in, it<br>
> might have python modules/packages that conflict with chimera's. <br>
> Or it might something in the environment. Chimera tries to<br>
> protect its python from the user's environment, but maybe we<br>
> missed something. Also double check that the chimera you're<br>
> invoking is the one you're expecting -- try using an absolute path<br>
> to chimera while you're debugging this.<br>
><br>
> HTH,<br>
><br>
> Greg<br>
><br>
><br>
> On 06/20/2016 01:18 PM, Subha Kalyaanamoorthy wrote:<br>
>> Hi There,<br>
>><br>
>> I am trying to call a script with Chimera commands(saved as<br>
>> sample.py file) in another python program using<br>
>> os.system("chimera --nogui --nostats sample.py") and I get an<br>
>> module load error as below,<br>
>><br>
>> import chimera<br>
>><br>
>> ImportError: No module named chimera<br>
>><br>
>><br>
>> However, if I call the script with chimera it works, for eg.,<br>
>> chimera --nogui --nostats sample.py typed directly in terminal is<br>
>> working.<br>
>><br>
>><br>
>> Can anybody help fix this error?<br>
>><br>
>><br>
>> Thanks in advance,<br>
>><br>
>> Best Regards,<br>
>><br>
>> Subha<br>
>><br>
>><br>
>><br>
>><br>
>> _______________________________________________<br>
>> Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <<a href="mailto:Chimera-users@cgl.ucsf.edu">mailto:Chimera-users@cgl.ucsf.edu</a>><br>
>> Manage subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br>
><br>
><br>
><br>
><br>
> -- <br>
> Dr. Subha Kalyaanamoorthy<br>
> Post Doctoral Fellow<br>
> Faculty of Pharmacy and Pharmaceutical Sciences<br>
> University of Alberta<br>
> Edmonton, Canada.<br>
><br>
><br>
><br>
> _______________________________________________<br>
> Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<br>
> Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
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