Evan, 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) Cheers, Warren _____
From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@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/Pmw Base.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw Dialog.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/Pmw Dialog.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 self.runPsize() File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs _tools.py", line 1155, in runPsize size.runPsize(pdb_filename) File "/sw/share/xtal/bin/psize.py", line 267, in runPsize self.parseInput(filename) File "/sw/share/xtal/bin/psize.py", line 102, in parseInput self.parseLines(file.readlines()) 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.kantrow...@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 -------------------------------------------------------------------
