From: xavier s. <xsi...@gm...> - 2007-02-06 15:01:32
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Hi, I am using the pymol package provided with Debian testing (0.98+0.99r). When I am trying to run a script without the gui, i.e. pymol -c foo.pml, I get the following error : Traceback (most recent call last): File "/var/lib/python-support/python2.4/pymol//__init__.py", line 364, in= ? invocation.parse_args(pymol_argv) File "/var/lib/python-support/python2.4/pymol/invocation.py", line 270, in parse_args options.deferred.append("_do_spawn %s"%av.pop()) IndexError: pop from empty list I think I solved it by changing the last line of /usr/bin/pymol from python2.4 ${PYMOL_PATH}/__init__.py "$*" to python2.4 ${PYMOL_PATH}/__init__.py "$@" --X. ------------------------------------------ Xavier Siebert, Ph.D. Laboratoire de Microscopie =C9lectronique Structurale (room 6234) Institut de Biologie Structurale (IBS) J.P. Ebel UMR 5075, CNRS 41, rue Jules Horowitz F-38027 Grenoble - Cedex 1 France Tel : ++334.38.78.96.12 Fax : ++334.38.78.54.94 |
From: Andreas H. <ah...@bi...> - 2007-02-08 10:33:30
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Hi Xavier, we also stumbled over this error and resolved it in a similar fasion. Also we have sent a bug report to debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=3D409188 The problem is that "$*" sends all command line arguments as a single combined string to pymol's __init__.py. The bug was "introduced" in the new debian package, before there were no quotes. Best. Christof & Andreas xavier siebert wrote: >Hi, >I am using the pymol package provided with Debian testing (0.98+0.99r). >When I am trying to run a script without the gui, i.e. pymol -c >foo.pml, I get the following error : > >Traceback (most recent call last): > File "/var/lib/python-support/python2.4/pymol//__init__.py", line 364,= in ? > invocation.parse_args(pymol_argv) > File "/var/lib/python-support/python2.4/pymol/invocation.py", line >270, in parse_args > options.deferred.append("_do_spawn %s"%av.pop()) >IndexError: pop from empty list > >I think I solved it by changing the last line of /usr/bin/pymol from >python2.4 ${PYMOL_PATH}/__init__.py "$*" >to >python2.4 ${PYMOL_PATH}/__init__.py "$@" > >--X. > >------------------------------------------ >Xavier Siebert, Ph.D. > >Laboratoire de Microscopie =C9lectronique Structurale (room 6234) >Institut de Biologie Structurale (IBS) J.P. Ebel >UMR 5075, CNRS >41, rue Jules Horowitz >F-38027 Grenoble - Cedex 1 >France > >Tel : ++334.38.78.96.12 >Fax : ++334.38.78.54.94 > >------------------------------------------------------------------------= - >Using Tomcat but need to do more? Need to support web services, security= ? >Get stuff done quickly with pre-integrated technology to make your job e= asier. >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geroni= mo >http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 121642 >_______________________________________________ >PyMOL-users mailing list >PyM...@li... >https://lists.sourceforge.net/lists/listinfo/pymol-users > =20 > --=20 Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: ah...@bi... |