Dear PyMOL users,
I'm in trouble in using APBS plugin to display the molecular surface.
The calculations of "set Grid" and "Run APBS" were successfully finished,
but showing the surface by the button of "show" in the Visualization (1) tab
fails with the following message
ObjectMapLoadDXFile: Loading from
'/Users/yoshitaka/Desktop/pymol-generated.dx'.
DXStrToMap: Dimensions: 97 129 129
DXStrToMap: Origin -31.288 -19.104 -13.876
DXStrToMap: Grid 0.484 0.497 0.462
DXStrToMap: 1614177 data points.
<type 'exceptions.ValueError'> Exception in Tk callback
Function: <bound method VisualizationGroup.showMolSurface of
<pmg_tk.startup.apbsplugin.VisualizationGroup instance at 0x1077ca3f8>> (type:
<type 'instancemethod'>)
Args: ()
Traceback (innermost last):
File "/usr/local/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py",
line 1747, in __call__
return apply(self.func, args)
File
"/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py",
line 2433, in showMolSurface
self.updateMolSurface()
File
"/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py",
line 2471, in updateMolSurface
self.updateRamp()
File
"/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py",
line 2458, in updateRamp
ramp_name = self.getRampName()
File
"/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py",
line 2440, in getRampName
idx = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i) ==
'object:molecule'].index(self.molecule.getvalue())
<type 'exceptions.ValueError'>: '' is not in list
Please tell me how to solve this plobrem.
I describe my settings as follows:
machine: Mac OS X 10.9.4, Intel Core i7, 16GB.
Xquartz is installed. The versions of gcc and g++ compilers are 4.8.1.
I installed tcl/tk (ver. 8.5.15), python (ver. 2.7.8), pmw (ver. 1.3.3), and
PyMOL (ver. 1.7.1.3) by using Homebrew.
brew uninstall python tcl-tk pmw pymol
brew tap homebrew/dupes
brew tap homebrew/science
brew install homebrew/dupes/tcl-tk --enable-threads --with-x11
brew install python --with-brewed-tk
brew install pymol
Next, I installed openmpi 1.8.1 in this way:
brew install openmpi
cd /usr/lib/
sudo ln -s /usr/local/Cellar/open-mpi/1.8.1/lib/libmpi.1.dylib libmpi.0.dylib
sudo ln -s /usr/local/Cellar/open-mpi/1.8.1/lib/libopen-rte.7.dylib
libopen-rte.0.dylib
sudo ln -s /usr/local/Cellar/open-mpi/1.8.1/lib/libopen-pal.6.dylib
libopen-pal.0.dylib
APBS and PDB2PQR binaries were employed from "APBS-1.4-osx.tar.gz" and
"pdb2pqr-osx-bin-1.9.0.tar.gz", respectively.
The plugin "apbsplugin.py" was downloaded from
"http://www.pymolwiki.org/index.php/Apbsplugin";.
The environment variable "DYLD_FALLBACK_LIBRARY_PATH" was set as
"/usr/local/Cellar/open-mpi/1.8.1/lib:/Users/yoshitaka/apps/APBS-1.4-osx/lib:$DYLD_FALLBACK_LIBRARY_PATH"
for the calculation.
Thank you for your help.
Yoshitaka
**********************************************************
Yoshitaka Moriwaki
Dept. of Biotechnology, Grad. Sch. of Agri. and Life Sci.,
The Univ. of Tokyo
**********************************************************
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