[Chimera-users] Module import error

[Greg Couch]

Just to follow up on the chimera-users list, the bug was in the script 
that invoked chimera via os.system("chimera ....").  It had an "import 
chimera" in it, which failed and wouldn't have helped anyway since 
chimera was being used as an external program, not as a module.

     -- Greg

On 06/20/2016 03:50 PM, Greg Couch wrote:
> 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
>>>
>>>
>>>
>>>
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>>
>>
>>
>>
>> -- 
>> Dr. Subha Kalyaanamoorthy
>> Post Doctoral Fellow
>> Faculty of Pharmacy and Pharmaceutical Sciences
>> University of Alberta
>> Edmonton, Canada.
>>
>>
>>
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>
>
>
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