1. January 12, 2015- Summary: Some RNA models do not fully construct in Ribbons and other ladder modes.
    1. Problem description: There are new atoms types/missing atoms in these models that were not recognized by earlier versions of the PMV software underlying ePMV. For example only chains A and B show up in model 4oo8.pdb cas-9 structure
    2. Solution for Ribbon representation: 
      1. In a few weeks you can update your ePMV software to solve this problem automatically
      2. To fix this manually, you must replace the two files and with these two new versions (the files reside in a folder called Pmv at /Users/YourName/Library/Preferences/MAXON/CINEMA4D R.../plugins/mgl64/MGLToolsPckgs/Pmv or C:\Documents and Setting\$username\Application Data\MAXON\CINEMA4D R12\plugins\ mgl64\MGLToolsPckgs\Pmv:
  • If you did not install your host software into one of the standard locations shown below, try to set the path manually by browsing:
  1. .blender for blender (see [2])
  2. Cinema4D R11.5 : /Application/MAXON/Cinema4D R11.5/plugins/Py4D/
  3. Cinema4D R12 : /Users/YourName/Library/Preferences/MAXON/CINEMA4D R12/plugins or C:\Documents and Setting\$username\Application Data\MAXON\CINEMA4D R12\plugins
  4. Maya 2011 : /Users/Shared/Autodesk/maya/2011/plug-ins/
  • Large molecule issue : before loading a large molecule, change the default option and uncheck the center molecule option as well as the bi-cylinder option. If this still not help loading the molecule, that means your reach the limits. Moreover, we found a segmentation fault while using the mslib (molecular surface, and surface area computing library) on large molecule.
  • Cinema4D R13 : folding any of the options in the window removes the submenu/options from being shown altogether. Only way to get them back is to close the window and reopen from plugins menu. This bug was report to MAXON, as it has nothing to do with ePMV.



  • Verify that you have move ePMV and pyubic int the MGLTools library folder and not the MGLTools application folder (/Application/MGL vs /Library/MGLTools) in the case you have used the MGLTools installer.

Cinema4D R12

  • Trying to create joints for a too large protein kill C4D. As well as converting the spline to joints




  • Script error at ePMV starting : check the blender console for the error message. Most of the time the error is related to a directory string which is not recognize by Python. For instance, the MGLToolsPckgs directory should be in a directory that have a caracter with accent, or in the root directory (e.g. C:\MGLToolsPckgs).
  • Run timer error at ePMV starting : If you encounter this error trying to call ePMV, simply click OK. A second similar windows should appear, and again click OK. You should now see the ePMV gui in the script windows.

Image:BlenderError1_win.jpg Image:BlenderError1_vista.jpg

Cinema4D R12

  • Windows Vista and probably 7 : numpy can't be currently imported (multiarray module not Found error). The solution we found, is to replace the actual python.framework of C4D by Python2.6.6 for Windows. This patch is part of the new installation procedure. The counter-part is that we loose a optimized python for c4d and this can bring some instability....For instance first time the plugin is launched the windows stay blank....

All host

  • Run timer error at host application termination or ePMV termination. This error can happen, we are trying to identify the problem, but you can still use ePMV.



  • import numpy : undefined symbol: _PyUnicodeUCS4_IsWhitespace
Your numpy is compiled for a UCS4 build of Python. But you have a UCS2 build of Python. Rebuild one of them to match up with the other. See also here for PyUnicodeUCS2*. This error seems to happen less often with the latest build of MGLTools (after November, 30).
  • ImportError: No module named _md5 or ImportError: or some other import error related to library.
This mean that the python interpreter cant find the required library. A easy way to fix this is to modify the plugin file which define the path to add to the python path. For instance, append the following line sys.path.append(MGL_ROOT+'/lib/')  and sys.path.append(MGL_ROOT+'/lib/python2.5/') in ( line59) that you can find in you .blender/scripts folder. The same can probably be apply to the

if sys.platform == "win32":
else :


Blender 2.6

  • if you encounter the following error, simply install libXss (sudo apt-get install libxss) :
error while loading shared libraries: cannot open shared object file: No such file or directory"


  • Atoms spheres rendering. There is a problem in shader connection initialisation. At creation time, if you render the atoms representation (or balls and stick), the sphere are not render, or only some a portion of the molecule is render. This can be fix by changing the material schems. The default colors is using the CPK rules, changing to "Per_residue" amd then back to "by atoms using CPK" will fix the shader connection problem and will let you render the atomic representation in all rendering modes. The same apply for the ball and stick representation.
  • Surface color. Molecular surface colors are pre-vertex which mean that in maya they will be render only using maya hardwar. The turnaround is to used a special mental ray shader node (see here) or to bake the color to a UV texture map (see tutorials).

Graham Johnson,
Jan 12, 2015, 1:54 PM
Graham Johnson,
Jan 12, 2015, 1:53 PM