apbs 1.0.0-2 CmdException in TK callback (Intrepid)

Bug #305225 reported by James on 2008-12-04
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
apbs (Ubuntu)
Undecided
Unassigned

Bug Description

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

James (jlara-cdc) wrote :

I'm closing this. The affected version is very old. Please reopen if you are still affected.

Changed in apbs (Ubuntu):
status: New → Incomplete
status: Incomplete → Fix Committed
status: Fix Committed → Incomplete
Changed in apbs (Ubuntu):
status: Incomplete → Invalid
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