This appears to be a problem with file format incompatibility between PyMOL and the psize.py script.  I suspect that rounding off the atom coordinates will eliminate it:
alter_state 1, all, (x,y,z)=(int(x*1000)/1000.0, int(y*1000)/1000.0, int(z*1000)/1000.0)

From: pymol-users-bounces@lists.sourceforge.net [mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf Of Evan Kantrowitz
Sent: Friday, September 21, 2007 7:28 AM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Pymol apbs problem

With a certain file 1za1 from pdb when I try to run apbs I get the errors below. Other files are OK. Any suggestions?

error: 1
ValueError Exception in Tk callback
Function: <function <lambda> at 0x182892b0> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/PmwDialog.py", line 153, in <lambda>
command=lambda self=self, name=name: self._doCommand(name))
File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/PmwDialog.py", line 132, in _doCommand
return command(name)
File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1111, in execute
File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1155, in runPsize
File "/sw/share/xtal/bin/psize.py", line 267, in runPsize
File "/sw/share/xtal/bin/psize.py", line 102, in parseInput
File "/sw/share/xtal/bin/psize.py", line 116, in parseLines
self.q = self.q + float(words[3])
ValueError: invalid literal for float(): 1.00101.59

Evan R. Kantrowitz, Ph.D evan.kantrowitz@bc.edu
Boston College Tel. 617-552-4558
Department of Chemistry FAX 617-552-2705
Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow
Chestnut Hill, MA 02467