Hi there,
I'm having problems visualising apbs .dx maps in pymol. Pymol (0.97)
and apbs (0.3.1) compile from source fine and run otherwise normally.
apbs_tools launches ok within pymol and the user interface appears fine.
On initiating the calculation, pink dots representing charge assignment appear
and disappear. apbs_tools output seems fine:
This executable compiled on Mar 18 2005 at 18:20:06
Parsing input file pymol-generated.in...
Parsed input file.
Got PQR 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.
2145 atoms
Centered at (-1.215e-01, 1.816e+00, -1.078e+00)
Net charge -2.99e+00 e
Preparing to run 2 PBE calculations.
----------------------------------------
CALCULATION #1: MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 191.244 MB total, 191.244 MB high water
Using cubic spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.689 x 0.704 x 0.761
Grid lengths: 66.183 x 67.631 x 73.076
Grid center: (-0.121, 1.833, -1.045)
Multigrid levels: 4
Molecule ID: 1
Nonlinear traditional PBE
Single Debye-Huckel sphere boundary conditions
4 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2.000 A-radius, 2.000 e-charge, 0.000 M concentration
2.000 A-radius, -2.000 e-charge, 0.000 M concentration
Solute dielectric: 20.000
Solvent dielectric: 80.000
Using "molecular" surface definition; harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 310.000 K
Surface tension: 0.105 kJ/mol/A^2
Solving PDE (see io.mc* for details)...
----------------------------------------
CALCULATION #2: MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 0 A
Current memory usage: 188.714 MB total, 216.587 MB high water
Using cubic spline charge discretization.
Grid dimensions: 97 x 97 x 97
Grid spacings: 0.614 x 0.623 x 0.656
Grid lengths: 58.931 x 59.783 x 62.986
Grid center: (-0.121, 1.833, -1.045)
Multigrid levels: 4
Molecule ID: 1
Nonlinear traditional PBE
Boundary conditions from focusing
4 ion species (0.000 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.000 M concentration
2.000 A-radius, -1.000 e-charge, 0.000 M concentration
2.000 A-radius, 2.000 e-charge, 0.000 M concentration
2.000 A-radius, -2.000 e-charge, 0.000 M concentration
Solute dielectric: 20.000
Solvent dielectric: 80.000
Using "molecular" surface definition; harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 310.000 K
Surface tension: 0.105 kJ/mol/A^2
Potential to be written to pymol-generated.dx
Solving PDE (see io.mc* for details)...
Writing potential to pymol-generated.dx
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage: 0.000 MB total, 216.587 MB high water
Thanks for using APBS!
ObjectMapLoadDXFile: Loading from 'pymol-generated.dx'.
DXStrToMap: Dimensions: 97 97 97
DXStrToMap: Origin -29.587 -28.058 -32.538
DXStrToMap: Grid 0.614 0.623 0.656
DXStrToMap: 912673 data points.
ObjectMap: Map Read. Range = -52.501362 to 43.938789
but the following error appears when I try to update under the
visualisation tab of apbs_tools:
Function: <bound method VisualizationGroup.refresh of
<pmg_tk.startup.apbs_tools.VisualizationGroup instance at 0x11fe808>>
(type: <type 'instance method'>)
Args: ()
Traceback (innermost last):
File "/usr/lib64/python2.2/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
line 1747, in __call__
return apply(self.func, args)
File "/usr/lib64/python2.2/site-packages/pmg_tk/startup/apbs_tools.py",
line 484, in refresh
getattr(self,thing).destroy()
File
"/usr/lib64/python2.2/site-packages/Pmw/Pmw_1_2/lib/PmwButtonBox.py", line
66, in destroy
Pmw.MegaWidget.destroy(self)
File "/usr/lib64/python2.2/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
line 386, in destroy
del _hullToMegaWidget[self._hull]
KeyError:
.17266312.17274344.17632616.18843560.17281704.18873128.18870664.18892984
I guess this is prob a more general python error within my setup but was
just wondering if anyone else has encountered this problem or has any
suggestions?
Thanks,
Nicola
--
Dr Nicola Meenan
Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3QU
T: +44 (0) 1865 275773
F: +44 (0) 1865 275253
