Public bug reported:
Binary package hint: apbs
When trying to 'show' Positive or Negative Isosurface, apbs throws the
following Cmdexceptions:
CmdException Exception in Tk callback
Function: <bound method VisualizationGroup.showPosSurface of
<pmg_tk.startup.apbs_tools.VisualizationGroup instance at 0xa7f42cc>> (type:
<type 'instancemethod'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line
1747, in __call__
return apply(self.func, args)
File "/var/lib/python-support/python2.5/pmg_tk/startup/apbs_tools.py", line
658, in showPosSurface
self.updatePosSurface()
File "/var/lib/python-support/python2.5/pmg_tk/startup/apbs_tools.py", line
663, in updatePosSurface
pymol.cmd.isosurface('iso_pos',self.map.getvalue(),float(self.pos_surf_val.getvalue()))
File "/var/lib/python-support/python2.5/pymol/creating.py", line 526, in
isosurface
if _self._raising(r,_self): raise pymol.CmdException
CmdException: <pymol.CmdException instance at 0xbf812ec>
CmdException Exception in Tk callback
Function: <bound method VisualizationGroup.showNegSurface of
<pmg_tk.startup.apbs_tools.VisualizationGroup instance at 0xa7f42cc>> (type:
<type 'instancemethod'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line
1747, in __call__
return apply(self.func, args)
File "/var/lib/python-support/python2.5/pmg_tk/startup/apbs_tools.py", line
667, in showNegSurface
self.updateNegSurface()
File "/var/lib/python-support/python2.5/pmg_tk/startup/apbs_tools.py", line
672, in updateNegSurface
pymol.cmd.isosurface('iso_neg',self.map.getvalue(),float(self.neg_surf_val.getvalue()))
File "/var/lib/python-support/python2.5/pymol/creating.py", line 526, in
isosurface
if _self._raising(r,_self): raise pymol.CmdException
CmdException: <pymol.CmdException instance at 0xbf810ac>
In addition the following error occurred during apbs run:
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from pymol-generated.pqr.
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
19190 atoms
Centered at (2.291e+01, 6.646e+01, 1.104e+02)
Net charge 2.00e+00 e
Preparing to run 2 PBE calculations.
I also tried running the apbs 'quicktest':
This executable compiled on Oct 8 2008 at 15:58:43
Parsing input file quicktest...
Vio_ctor2: some error occurred.
Vio_ctor: Vio_ctor2() failed.
Error while opening input file quicktest!
Full description of run is attached. Help on how to resolve this issue is
greatly appreciated. Best Regards,
James
** Affects: apbs (Ubuntu)
Importance: Undecided
Status: New
--
apbs 1.0.0-2 CmdException in TK callback (Intrepid)
https://bugs.launchpad.net/bugs/305225
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