I've been using the APBS plugin the last couple days and have noticed a
bug in the behavior of the plugin. This is using the hybrid X11 version
of PyMOL 0.97 on OSX 10.3.5 and Apple's X11.
After starting X11, I click the PyMOLX11Hybrid icon and select the APBS
plugin from the tcl GUI. Looking at the tab "APBS Location", the location
for the apbs binary is not filled in (the binary is at
/usr/local/bin/apbs). I can fill that in manually and everything works
However, the apbs location is not saved. Setting APBS_BINARY in either
~/.bash_profile, ~/.bashrc, or /etc/bashrc does not help. While both
Terminal.app and xterms show that APBS_BINARY is set, PyMOL is not seeing
this as being set.
However, if I open PyMOL by typing "open
~/Applications/PyMOLX11Hybrid.app" in either an xterm or Terminal.app,
then PyMOL does automatically see the location of apbs.
This seems to me the result of PyMOL using X11.app's environment and not
the environment of a normal shell when run by clicking the icon. Is this
a reasonable assumption? Could someone with XDarwin and apbs try this?
I no longer have a Mac with XDarwin, but with other stuff, XDarwin always
read the environment normally.
If this is a problem with Apple's X11 and PyMOL, can PyMOL be modified to
work around this? The issue is not critical in this case and there's a
simple workaround, but I could see it causing problems for other things
that expect a normal environment.
And when the last last law was down, and the Devil turned round on
you - where would you hide, Roper, the laws all being flat?
--Robert Bolt, "A Man For All Seasons"
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