#93 Tcl/Tk GUI fails after opening APBS plugin mac osx

[Alejandro Buschiazzo]

Under OSX 10.4.11, fink installation of pymol-py26 works fine, until the APBS window is triggered as a pymol plugin. Immediately, Pymol's Tcl/Tk GUI becomes 'unclickable', even after closing the APBS window again. Only solution seems to quit and restart PyMol.
Seems to be something to do with X11 (using X11 1.1.3 - XFree86 4.4.0)? I am not able to find the way to update to a newer X11 version (if it is at all possible for Tiger 10.4.....)
My Mac is an Intel Macbook Pro 17" laptop; OpenGL graphics : ATI Radeon X1600 (GL version 2.0 ATI-1.4.56)
Any suggestion will be highly appreciated

[Michael Lerner]

Can you try out the latest version of the plugin? You can find it here:
http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py?view=log

(click on either "download" or "as text"). You can install it via the plugin menu and it'll show up as APBS Tools 2. Please let me know if it works for you.

[Alejandro Buschiazzo]

Hi Michael, thank you for the suggestion.....I tried it, the new plugin is now indeed visible as "APBS Tools 2"
But, when I try to run it, I get this whole bunch of errors :

Error: 1
<type 'exceptions.OSError'> Exception in Tk callback
Function: <function <lambda> at 0x2179d8f0> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File "/sw/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "/sw/lib/pymol-py25/modules/pmg_tk/startup/apbsplugin.py", line 221, in <lambda>
command = lambda s=self: APBSTools2(s))
File "/sw/lib/pymol-py25/modules/pmg_tk/startup/apbsplugin.py", line 781, in __init__
value = get_default_location('apbs.exe'),
File "/sw/lib/pymol-py25/modules/pmg_tk/startup/apbsplugin.py", line 204, in get_default_location
if os.path.exists(f) and verify(name,f):
File "/sw/lib/pymol-py25/modules/pmg_tk/startup/apbsplugin.py", line 163, in verify
(retcode,prog_out) = run(f,'--version')
File "/sw/lib/pymol-py25/modules/pmg_tk/startup/apbsplugin.py", line 250, in run
retcode = subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
File "/sw/lib/python2.5/subprocess.py", line 444, in call
return Popen(*popenargs, **kwargs).wait()
File "/sw/lib/python2.5/subprocess.py", line 594, in __init__
errread, errwrite)
File "/sw/lib/python2.5/subprocess.py", line 1097, in _execute_child
raise child_exception
<type 'exceptions.OSError'>: [Errno 13] Permission denied

I will greatly appreciate your help here!
alejandro

[Michael Lerner]

That is a particularly strange error.

Just to verify, you downloaded the plugin sometime after Friday night? (I released a new version then.)

I've been testing the native PyMOL builds under OS X 10.6. I don't have a 10.4 system around, but I'll try out the fink build, hoping that the problem lies with fink rather than with 10.4.

[Nobody/Anonymous]

Yes, I downloaded the plugin yesterday (Saturday)....
I appreciate if you can look what happens under 10.4

[Nobody/Anonymous]

Unfortunately, I don't have a 10.4 system to test on.
I made a few more bug fixes, so you can try the newest version (download from the same place as before), but I'm not positive that it'll fix your issue. Can you try it out and let me know, though?

It's a little strange that your error message talks about python 2.5 when you installed pymol-py2.6.

Here's exactly what I did to get a working system on 10.6:

(Install Fink and PyMOL)

Download the fink source tarball from http://www.finkproject.org/download/srcdist.php
tar xvfz fink-0.29.10.tar
cd fink-0.29.10
./bootstrap
/sw/bin/pathsetup.sh

(open a new terminal)

fink selfupdate
fink install pymol-py26

(activate the unstable branch and install pdb2pqr)

sudo perl -pi.bak -e 's| stable/main | stable/main unstable/main unstable/crypto |g' /sw/etc/fink.conf
fink selfupdate-rsync; fink scanpackages; sudo apt-get update
fink install pdb2pqr

(Turn off the unstable branch)

sudo cp /sw/etc/fink.conf.bak /sw/etc/fink.conf
fink index