Hello Stuart,
By default, alter_state expressions are evaluated in the "pymol"
namespace of the current PyMOL instance, not the "cmd" (pymol.cmd)
namespace. The reason why it works with 'run' is that run also executes
in "pymol" by default, and thus, includes any functions you define.
Try:
cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z],
stored.tmpOp)")
instead, after using cmd.extend in your startup or GUI script.
Cheers,
Warren
________________________________
From: Stuart Ballard [mailto:srball...@wisc.edu]
Sent: Monday, August 24, 2009 3:38 PM
To: pymol-users
Subject: [PyMOL] Calling scripted functions within alter_state
Hello Warren, all,
I've been working on a plugin for PyMOLX11Hybrid, in which I have a few
lines of code such as:
cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z],
stored.tmpOp)")
AND
cmd.alter_state(1, object, "x,y,z =
cell_shift_helper([x,y,z],stored.shift)")
Both those functions (sym_partner and cell_shift_helper) are extended
through cmd.extend() function, along with several others which work
perfectly well. The issue arises only when I attempt to use these
functions through a menu added to PyMOL GUI, which does not involve
issuing the run /(filepath)/(script).py command in PyMOL, but rather
initializes necessary commands on startup. I've confirmed that the
cmd.extend() calls are made properly, but I can only fix the problem by
issuing the run command independent of my initialization scripts.
Because this script is planned to be incorporated into a build of PyMOL
which will be run from a variety of file paths, I'd like to know how I
can solve this problem without simply jury rigging a run command. Is
there a way to properly make commands available within an alter_state
command without using the run command?
Thanks,
Stuart Ballard
Dept. of Biochemistry
UW-Madison
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