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=409188
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 Électronique Structurale (room 6234)
Institut de Biologie Structurale (IBS) J.P. Ebel
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41, rue Jules Horowitz
F-38027 Grenoble - Cedex 1
France
Tel : ++334.38.78.96.12
Fax : ++334.38.78.54.94
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Andreas Henschel
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