The Molecular Graphics Laboratory Forum

Hi there,

I've tried installing ePMV on Ubuntu 10.10 using the system-supplied version of Blender (2.49b for python 2.6). I can install the ePMV plugin fine, but it fails to open as the version of numpy in the supplied python libraries has been compiled with the wrong unicode option (undefined symbol: PyUnicodeUCS2_FromUnicode). If I change the search path order in ~/.blender/scripts/epmv_blender_plugin.py to append '/lib/python2.5/site-packages' at the end of sys.path instead of the beginning (so I use the system-supplied numpy) the plugin starts but the layout is all screwy and it crashes almost immediately.

Is there a way to install MGLTools and ePMV to use my native python 2.6.6 install rather than its own pre-compiled python 2.5 binary, so I can use the system-supplied version of Blender? Is the version of mgltools present in the Ubuntu repos (1.5.4.cvs.20090603-1.1) recent enough for ePMV to run, or are more recent backports available? Alternatively, is there an easy way to get Blender 2.49b python 2.5 install without trashing my system-wide python paths?

Thanks,

Stephen

Hi Stephen,

well that's a tricky one, the problem is that MGLTools rely on python 2.5 and its not pure python. So trying to call python module compiled for python2.5 in a python2.6 environment will crash on Linux.
A workaround would be to recompile all dependent packages of MGLTools with your python 2.6.6 installation, and this can be tough but doable (I can guide you if you are interested). But we may have a MGLTools version working with python2.6 which may solve this problem, but I need to check that with the mgl developers, and if I can provide it to you..

>>Alternatively, is there an easy way to get Blender 2.49b python 2.5 install without trashing my system-wide python paths?
You can compile a local python2.5 and use it for building blender 2.49b or try to use the local python that ship with MGLTools.

Ludovic

Hi Ludovic,

Thanks for that. I though the latter option would probably be the easiest (use the version of python distributed with MGLTools). It's easy enough to download the appropriate version of blender (http://download.blender.org/release/Ble ... 86.tar.bz2) and set up all the python paths to point to that distributed with MGLTools (I just cribbed the launch script for PMV, which works fine on my machine). However, it seems like when they're building the install bundle for MGLTools they don't include the python shared libaries (libpython2.5.so.1.0), which means blender can't launch...

So I tried instead to compile MGLTools from source (http://mgltools.scripps.edu/downloads/t ... rc2.tar.gz). This seemed to install and compile fine once I modified the first line of InstTools/install to run my version of python. However, when I try and runPmv I get the following error:

Run PMV from /home/stepheng/bin/mgltools/MGLToolsPckgs/Pmv
Resource file used to customize PMV: /home/stepheng/.mgltools/1.5.6rc2/Pmv/_pmvrc
Traceback (most recent call last):
File "/home/stepheng/bin/mgltools/MGLToolsPckgs/Pmv/__init__.py", line 381, in runPmv
title=title, withShell= not interactive, verbose=False, gui=gui)
File "/home/stepheng/bin/mgltools/MGLToolsPckgs/Pmv/moleculeViewer.py", line 840, in __init__
trapExceptions=trapExceptions)
File "/home/stepheng/bin/mgltools/MGLToolsPckgs/ViewerFramework/VF.py", line 369, in __init__
self.GUI = ViewerFrameworkGUI(self, title=title,
NameError: global name 'ViewerFrameworkGUI' is not defined

If I modify MGLToolsPckgs/Pmv/moleculeViewer.py to include the line:
from ViewerFramework.VFGUI import ViewerFrameworkGUI
Then things seems to work find (assuming I have the python IDE 'idle' installed...took a while to find that dependency!) and I can run PMV. I can even install the ePMV plugin in blender. However, if I restart blender and then try and run the script I get a load of errors at the console (below).

It seems like I'm pretty close, so any help get me there would be most appreciated.

Thanks,

Stephen


=== Blender console output ===
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0xb0593cc>> ignored
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0xb0594cc>> ignored
Compiled with Python version 2.6.6.
Checking for installed Python... got it!
MSMSLIB 1.4.4 started on nimbus
Copyright M.F. Sanner (March 2000)
Compilation flags
try to restore
None
Resource file used to customize PMV: /home/stepheng/.mgltools/1.5.6rc2/Pmv/_pmvrc
[(0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.54000000000000004, 0.54000000000000004, 0.54000000000000004), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.51000000000000001, 1.0, 0.0), (0.41999999999999998, 0.22, 0.76000000000000001), (0.84999999999999998, 0.84999999999999998, 0.84999999999999998), (0.63, 0.5, 1.0), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.27000000000000002, 0.52000000000000002, 0.11), (0.90000000000000002, 0.10000000000000001, 0.10000000000000001), (0.20000000000000001, 0.33000000000000002, 1.0), (1.0, 0.58999999999999997, 0.0), (0.94999999999999996, 0.84999999999999998, 0.0), (0.69999999999999996, 0.90000000000000002, 0.20000000000000001), (0.27000000000000002, 0.52000000000000002, 0.11), (0.59999999999999998, 0.23000000000000001, 0.080000000000000002), (0.63, 0.5, 1.0), (0.27000000000000002, 0.52000000000000002, 0.11), (0.27000000000000002, 0.52000000000000002, 0.11), (0.27000000000000002, 0.52000000000000002, 0.11), (0.27000000000000002, 0.52000000000000002, 0.11), (0.34000000000000002, 0.79000000000000004, 1.0), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.51000000000000001, 1.0, 0.0), (0.63, 0.5, 1.0), (0.51000000000000001, 1.0, 0.0), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.82999999999999996, 0.40000000000000002, 0.0), (0.59999999999999998, 0.23000000000000001, 0.080000000000000002), (0.63, 0.5, 1.0), (0.63, 0.5, 1.0), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005), (0.94999999999999996, 0.72999999999999998, 0.56000000000000005)]
[(0.78100000000000003, 0.78100000000000003, 0.78100000000000003), (0.91800000000000004, 0.91800000000000004, 0.91800000000000004), (0.85899999999999999, 0.58599999999999997, 0.50800000000000001), (0.058999999999999997, 0.50800000000000001, 0.058999999999999997), (0.058999999999999997, 0.50800000000000001, 0.058999999999999997), (0.058999999999999997, 0.50800000000000001, 0.058999999999999997), (0.89800000000000002, 0.89800000000000002, 0.0), (0.89800000000000002, 0.89800000000000002, 0.0), (0.97699999999999998, 0.58599999999999997, 0.0), (0.97699999999999998, 0.58599999999999997, 0.0), (0.89800000000000002, 0.039, 0.039), (0.89800000000000002, 0.039, 0.039), (0.70299999999999996, 0.35199999999999998, 0.70299999999999996), (0.50800000000000001, 0.50800000000000001, 0.81999999999999995), (0.0, 0.89800000000000002, 0.89800000000000002), (0.0, 0.89800000000000002, 0.89800000000000002), (0.078, 0.35199999999999998, 0.999), (0.078, 0.35199999999999998, 0.999), (0.19500000000000001, 0.19500000000000001, 0.66400000000000003), (0.19500000000000001, 0.19500000000000001, 0.66400000000000003), (1, 0, 0), (1, 1, 0), (0, 0, 1), (0, 1, 0), (1, 0.5, 0)]
[(1.0, 1.0, 1.0), (0.69999999999999996, 0.69999999999999996, 1.0), (1.0, 1.0, 1.0), (1.0, 1.0, 1.0), (1.0, 0.69999999999999996, 0.69999999999999996), (1.0, 0.69999999999999996, 0.69999999999999996), (1.0, 0.69999999999999996, 0.69999999999999996), (1.0, 0.69999999999999996, 0.69999999999999996), (1.0, 0.69999999999999996, 0.69999999999999996), (0.69999999999999996, 0.69999999999999996, 1.0), (0.69999999999999996, 0.69999999999999996, 1.0), (0.69999999999999996, 0.69999999999999996, 1.0), (0.69999999999999996, 0.69999999999999996, 1.0), (0.69999999999999996, 0.69999999999999996, 1.0), (0.699999999Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0xb722c4c>> ignored
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0xb72868c>> ignored

Warning (from warnings module):
File "/home/stepheng/bin/mgltools/MGLToolsPckgs/ViewerFramework/customizationCommands.py", line 132
DeprecationWarning)
DeprecationWarning: Show Progress Bar user preference is deprecated. Please update your resource files.
>>>
Warning (from warnings module):
File "/home/stepheng/bin/mgltools/MGLToolsPckgs/AutoDockTools/autoanalyzeCommands.py", line 75
import types, Tkinter, commands, os, copy, glob, popen2, time
DeprecationWarning: The popen2 module is deprecated. Use the subprocess module.
>>> 99999996, 0.69999999999999996, 1.0), (0.69999999999999996, 0.69999999999999996, 1.0), (0.69999999999999996, 0.69999999999999996, 1.0), (0.69999999999999996, 0.69999999999999996, 1.0), (0.90000000000000002, 0.84999999999999998, 0.10000000000000001), (0.90000000000000002, 0.84999999999999998, 0.10000000000000001), (1.0, 0.20000000000000001, 0.20000000000000001), (1.0, 0.20000000000000001, 0.20000000000000001), (1.0, 0.20000000000000001, 0.20000000000000001), (1.0, 0.20000000000000001, 0.20000000000000001), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0), (0.20000000000000001, 0.29999999999999999, 1.0)]
[(0.996, 0.996, 0.0), (0.996, 0.11700000000000001, 0.11700000000000001), (0.996, 0.48399999999999999, 0.053999999999999999), (0.996, 0.55800000000000005, 0.55800000000000005), (0.19500000000000001, 0.19500000000000001, 0.996), (0.183, 0.308, 0.183), (0.75, 0.75, 0.75), (0.996, 0.32800000000000001, 0.053999999999999999), (0.72199999999999998, 0.28100000000000003, 0.24199999999999999), (0.11700000000000001, 0.70299999999999996, 0.11700000000000001), (0.93700000000000006, 0.93700000000000006, 0.93700000000000006), (0.39000000000000001, 0.75700000000000001, 0.996), (0.70299999999999996, 0.078, 0.039), (0.41699999999999998, 0.55400000000000005, 0.13600000000000001), (0.222, 0.222, 0.40600000000000003), (0.42899999999999999, 0.105, 0.097000000000000003), (0.0, 0.996, 0.0), (0.73399999999999999, 0.55800000000000005, 0.55800000000000005), (0.85499999999999998, 0.57399999999999995, 0.437), (0.57799999999999996, 0.57799999999999996, 0.066000000000000003)]
[(1.0, 1.0, 1.0), (0.0, 0.0, 0.0), (1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0), (0.0, 1.0, 1.0), (1.0, 1.0, 0.0), (1.0, 0.0, 1.0)]
[(1.0, 1.0, 1.0), (0.0, 0.0, 0.0), (1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0), (0.0, 1.0, 1.0), (1.0, 1.0, 0.0), (1.0, 0.0, 1.0)]
[(1.0, 1.0, 1.0), (0.0, 0.0, 0.0), (1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0), (0.0, 1.0, 1.0), (1.0, 1.0, 0.0), (1.0, 0.0, 1.0)]
[(1.0, 1.0, 1.0), (0.0, 0.0, 0.0), (1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0), (0.0, 1.0, 1.0), (1.0, 1.0, 0.0), (1.0, 0.0, 1.0)]
[(1.0, 1.0, 1.0), (0.0, 0.0, 0.0), (1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0), (0.0, 1.0, 1.0), (1.0, 1.0, 0.0), (1.0, 0.0, 1.0)]
[(0.375, 0.5, 1.0), (0.93700000000000006, 0.0, 0.5), (1.0, 1.0, 0.0), (1.0, 1.0, 1.0)]

WARNING: dependency check failed for command APBSVolumeRender
noModeller
noAutoFill
noARViewer
[(1.0, 0.5, 1.0), (0.0, 0.50900000000000001, 0.0), (1.0, 0.5, 0.5), (0.25, 0.75, 1.0), (0.51700000000000002, 0.25490000000000002, 0.25879999999999997), (1.0, 0.0, 1.0), (0.0, 0.75, 1.0), (0.0, 1.0, 0.5), (0.59999999999999998, 1.0, 0.0), (1.0, 0.5, 0.0), (1.0, 0.0, 0.5), (0.5, 0.0, 1.0), (0.5, 0.0, 0.20000000000000001), (0.0, 0.5, 0.20000000000000001), (0.75, 0, 1), (1.0, 0.75, 0), (1.0, 0.0, 0.75), (0.0, 1.0, 0.75), (1.0, 0.0, 0.25), (0.0, 0.5, 1.0)]
Traceback (most recent call last):
File "/home/stepheng/bin/mgltools/MGLToolsPckgs/ePMV/epmvGui.py", line 1123, in CreateLayout
self._createLayout()
File "/home/stepheng/bin/mgltools/MGLToolsPckgs/pyubic/uiAdaptor.py", line 466, in _createLayout
y=self._draw(block,y)
File "/home/stepheng/bin/mgltools/MGLToolsPckgs/pyubic/uiAdaptor.py", line 283, in _draw
self._drawElem(elem, x, y)
File "/home/stepheng/bin/mgltools/MGLToolsPckgs/pyubic/uiAdaptor.py", line 360, in _drawElem
self.drawImage(elem,x,y,w=w,h=h)
File "/home/stepheng/bin/mgltools/MGLToolsPckgs/pyubic/blender/blenderUI.py", line 1059, in drawImage
img = Blender.Image.Load(elem["value"])
IOError: couldn't load image
button string len: 8 0xb8b5530
button string len: 24 0xba91520
button string len: 104 0xba919a0
button string len: 92 0xba97020
button string len: 12 0xb44bdf8
button string len: 8 0xb8b3ef0
button string len: 4 0xb8c2d70
button string len: 4 0xb8c4348
pybutton str len: 104 0xa77a3e0
pybutton str len: 104 0xbb74a68
Saved session recovery to /home/stepheng/.blender/quit.blend
Error Totblock: 10

Blender quit

Hi Stephen,

you did a great job so far....
About your error :
img = Blender.Image.Load(elem["value"])
IOError: couldn't load image
I never saw this error, you can check if you actually have the image in MGLToolsPckgs/ePMV/images/banner.jpg
Another option is to edit the file MGLToolsPckgs/ePMV/epmvGui.py and comment out the line 1679:
self._layout.append([self.BANNER,])

this way you can go further and see whats else is broken ....

Ludovic

Hi Ludovic,

Thanks for that. I do have that jpeg image, so it's odd it won't load (perhaps a missing library on my part?). Anyway, when I comment out the load command as you suggested the ePMV then seems to start up fine and I can load a structure from the PDB. So it seems like I'm in business.

Thanks,

Stephen

P.S. For anyone interested, the error I got with MGLToolsPckgs/Pmv/moleculeViewer.py previously seemed actually due to not having python IDLE installed (?), so if you have all the correct libraries installed you don't need to change the MGLTools source at all to get PMV running. The only required change to get all the way is commenting out the append self.BANNER command in MGLToolsPckgs/ePMV/epmvGui.py

Hi,

I was just wondering how things were doing for you and epmv on linux...I hope you didnt encounter to many bug..
I was also wondering if you will be interested by getting the version for blender2.5.
I was able to get it work on mac, so it should not be too hard to get it running on linux...

Let me know if you are interested, and even better if you are willing to help...

Ludovic