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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.<br>
<br>
-- Greg<br>
<br>
<div class="moz-cite-prefix">On 06/20/2016 03:50 PM, Greg Couch
wrote:<br>
</div>
<blockquote cite="mid:5768733E.3060209@cgl.ucsf.edu" type="cite">
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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.<br>
<br>
-- Greg<br>
<br>
<div class="moz-cite-prefix">On 06/20/2016 03:27 PM, Subha
Kalyaanamoorthy wrote:<br>
</div>
<blockquote
cite="mid:CAFuN1V=PtjK=nBd6+-_4Tir1T+xc8JebJvx0frzbeoyqEUq1og@mail.gmail.com"
type="cite">
<div dir="ltr"><span style="font-size:13px">Hi Greg,</span>
<div style="font-size:13px"><br>
</div>
<div style="font-size:13px"><font face="verdana, sans-serif">Thanks
for the kind reply. </font></div>
<div style="font-size:13px"><font face="verdana, sans-serif">Sorry
about the typo.</font></div>
<div style="font-size:13px"><font face="verdana, sans-serif"><br>
</font></div>
<div style="font-size:13px"><font face="verdana, sans-serif">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. </font></div>
<div style="font-size:13px"><font face="verdana, sans-serif"><br>
</font></div>
<div style="font-size:13px"><font face="verdana, sans-serif">However,
calling the chimera script using "python sample.py"
doesn't work and using absolute path to chimera didn't
help too.</font></div>
<div style="font-size:13px"><font face="verdana, sans-serif"><br>
</font></div>
<div style="font-size:13px"><font face="verdana, sans-serif">I
tried installing pychimera, but end up with the same kind
of error when I try pychimera -i</font></div>
<div style="font-size:13px"><font face="verdana, sans-serif">import
pychimera</font></div>
<p style="font-size:13px;margin:0px;line-height:normal"><font
face="verdana, sans-serif">ImportError: No module named
pychimera</font></p>
<p style="font-size:13px;margin:0px;line-height:normal"><font
face="verdana, sans-serif"><br>
</font></p>
<p style="font-size:13px;margin:0px;line-height:normal"><font
face="verdana, sans-serif">Couldn't understand what's
going on with these import modules.</font></p>
<p style="font-size:13px;margin:0px;line-height:normal"><font
face="verdana, sans-serif"><br>
</font></p>
<p style="font-size:13px;margin:0px;line-height:normal"><font
face="verdana, sans-serif">I would greatly appreciate any
suggestions to solve this.</font></p>
<p style="font-size:13px;margin:0px;line-height:normal"><font
face="verdana, sans-serif"><br>
</font></p>
<p style="font-size:13px;margin:0px;line-height:normal"><font
face="verdana, sans-serif">Thanks,</font></p>
<p style="font-size:13px;margin:0px;line-height:normal"><font
face="verdana, sans-serif">Subha</font></p>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Jun 20, 2016 at 4:05 PM, Greg
Couch <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:gregc@cgl.ucsf.edu" target="_blank">gregc@cgl.ucsf.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> (I assume you meant
--nostatus)<br>
<br>
For me the simple test of a file with:<br>
<blockquote type="cite">import os<br>
os.system("chimera --nogui --nostatus")<br>
</blockquote>
works just fine. So it's probably something about your
particular setup that is tickling this bug.<br>
<br>
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.<br>
<br>
HTH,<br>
<br>
Greg
<div>
<div class="h5"><br>
<br>
<div>On 06/20/2016 01:18 PM, Subha Kalyaanamoorthy
wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div dir="ltr"><font face="verdana, sans-serif">Hi
There,</font>
<div><font face="verdana, sans-serif"><br>
</font></div>
<div><font face="verdana, sans-serif">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,</font></div>
<div><font face="verdana, sans-serif"><br>
</font></div>
<div>
<p style="margin:0px;line-height:normal"><span><font
face="verdana, sans-serif">import
chimera</font></span></p>
<p style="margin:0px;line-height:normal"><span><font
face="verdana, sans-serif">ImportError:
No module named chimera</font></span></p>
<p style="margin:0px;line-height:normal"><span><font
face="verdana, sans-serif"><br>
</font></span></p>
<p style="margin:0px;line-height:normal"><font
face="verdana, sans-serif">However, if I
call the script with chimera it works, for
eg., chimera --nogui --nostats sample.py
typed directly in terminal is working.</font></p>
<p style="margin:0px;line-height:normal"><font
face="verdana, sans-serif"><br>
</font></p>
<p style="margin:0px;line-height:normal"><font
face="verdana, sans-serif">Can anybody
help fix this error?</font></p>
<p style="margin:0px;line-height:normal"><font
face="verdana, sans-serif"><br>
</font></p>
<p style="margin:0px;line-height:normal"><font
face="verdana, sans-serif">Thanks in
advance,</font></p>
<p style="margin:0px;line-height:normal"><font
face="verdana, sans-serif">Best Regards,</font></p>
<p style="margin:0px;line-height:normal"><font
face="verdana, sans-serif">Subha</font></p>
<div><br>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">Dr. Subha Kalyaanamoorthy
<div>Post Doctoral Fellow</div>
<div>Faculty of Pharmacy and Pharmaceutical Sciences</div>
<div>University of Alberta</div>
<div>Edmonton, Canada.</div>
<div><br>
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