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PostPosted: Wed Mar 28, 2012 9:51 pm 
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glad it finally work...
about your problem with the glucose. Is is because the residue field of the PDB file is blank. I am using some naming rule that used the chain name when creating the geometry. I now fixed it, and it will be in the next update. But you can update manually the concerned file:
download the following file http://mgldev.scripps.edu/projects/ePMV/SOURCES/ePMV/comput_util.py and put it in :
C:\\Documents and Settings\\R\xe9\xad\xa9\\Application Data\\MAXON\\cinema 4d_34A33228\\plugins\ePMV\mgl32\MGLToolsPckgs\ePMV\
and if you use the 64bit version:
C:\\Documents and Settings\\R\xe9\xad\xa9\\Application Data\\MAXON\\cinema 4d_34A33228\\plugins\ePMV\mgl64\MGLToolsPckgs\ePMV\

Ludo


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PostPosted: Thu Mar 29, 2012 6:41 am 
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Thank you very much, I will test your file this evening after work.

I will tell you if it work for me.


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PostPosted: Thu Mar 29, 2012 4:28 pm 
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Hi,

Sorry, but i still have the same "Error" box when i try to load the glucose.pdb file !

I am disappointed, specially when i see the screenshot you've joined to your last message !


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PostPosted: Thu Mar 29, 2012 4:44 pm 
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Hi,

can you be more specific about the error you get?
after loading glucose.pdb did you see anything in the outliner ? if thew option says to produce a secondary structure at loading time this will cause an error as there is no secondary structure for a sugar, but your molecule will be still loaded and all the other representation will be available.
Verify the outliner, as well as the pulldown menu in ePMV.

Also can you show me what is the message in the console ?

Ludo


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PostPosted: Thu Mar 29, 2012 4:59 pm 
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Hello,

When I launch ePMV, i've got this ine the console :

C:\Documents and Settings\R魩\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\MGLToolsPckgs
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x0DC6F580>> ignored
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x0DC6F580>> ignored
execute
try to restore
None
<module 'c4d' (built-in)>
Resource file used to customize PMV: C:\Documents and Settings\R魩\.mgltools\latest\Pmv\_pmvrc
[(0.375, 0.5, 1.0), (0.93700000000000006, 0.0, 0.5), (1.0, 1.0, 0.0), (1.0, 1.0, 1.0)]
ERROR *********************************************
Traceback (most recent call last):
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\ViewerFramework\VF.py", line 898, in tryto
result = command( *args, **kw )
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\ViewerFramework\basicCommand.py", line 338, in doit
self.vf.addCommand( d['cmd'], d['name'], d['gui'])
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\ViewerFramework\VF.py", line 1288, in addCommand
command.onAddCmdToViewer()
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\Pmv\coarseMolSurfaceCommands.py", line 89, in onAddCmdToViewer
from DejaVu.VisionInterface.GeometryNodes import ConnectedComponents
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\DejaVu\VisionInterface\GeometryNodes.py", line 34, in <module>
from NetworkEditor.items import NetworkNode
ImportError: No module named NetworkEditor.items
WARNING: dependency check failed for command APBSVolumeRender
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x0E7E2058>> ignored
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x0E8C51C0>> ignored
[(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), (0.9499999999999999
, 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), (0.94
99999999999996, 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), (0.9769999999999
998, 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, 0.664000000
0000003), (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), (0.699999999999999
6, 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), (0.69999999999999996, 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.
0000000000000001, 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, 0.299999
9999999999, 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, 0.93700000000000
06), (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, 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)]
[(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)]
[(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)]
[(0.0, 0.0, 1.0), (0.0, 1.0, 0.0), (1.0, 0.0, 0.0), (0.0, 1.0, 1.0), (1.0, 1.0, 0.0), (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)]
[(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)]
noModeller
noAutoFill
noARViewer
no pymol
no prody
[(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)]


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PostPosted: Thu Mar 29, 2012 5:45 pm 
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can you post the rest of it, I don't see anything wrong here.
Ludo


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PostPosted: Thu Mar 29, 2012 7:15 pm 
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Here the same log, but i try to load the glucose.pdb molecule that is on my desk.


C:\Documents and Settings\R魩\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\MGLToolsPckgs
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x0D855580>> ignored
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x0D855580>> ignored
execute
try to restore
None
<module 'c4d' (built-in)>
Resource file used to customize PMV: C:\Documents and Settings\R魩\.mgltools\latest\Pmv\_pmvrc
[(0.375, 0.5, 1.0), (0.93700000000000006, 0.0, 0.5), (1.0, 1.0, 0.0), (1.0, 1.0, 1.0)]
ERROR *********************************************
Traceback (most recent call last):
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\ViewerFramework\VF.py", line 898, in tryto
result = command( *args, **kw )
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\ViewerFramework\basicCommand.py", line 338, in doit
self.vf.addCommand( d['cmd'], d['name'], d['gui'])
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\ViewerFramework\VF.py", line 1288, in addCommand
command.onAddCmdToViewer()
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\Pmv\coarseMolSurfaceCommands.py", line 89, in onAddCmdToViewer
from DejaVu.VisionInterface.GeometryNodes import ConnectedComponents
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\DejaVu\VisionInterface\GeometryNodes.py", line 34, in <module>
from NetworkEditor.items import NetworkNode
ImportError: No module named NetworkEditor.items
WARNING: dependency check failed for command APBSVolumeRender
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x16366558>> ignored
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x16622FD0>> ignored
[(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), (0.9499999999999999
, 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), (0.94
99999999999996, 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), (0.9769999999999
998, 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, 0.664000000
0000003), (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), (0.699999999999999
6, 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), (0.69999999999999996, 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.
0000000000000001, 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, 0.299999
9999999999, 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, 0.93700000000000
06), (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, 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)]
[(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)]
[(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)]
[(0.0, 0.0, 1.0), (0.0, 1.0, 0.0), (1.0, 0.0, 0.0), (0.0, 1.0, 1.0), (1.0, 1.0, 0.0), (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)]
[(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)]
noModeller
noAutoFill
noARViewer
no pymol
no prody
[(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)]
('action ', 'Browse', <bound method epmvGui.browsePDB of <ePMV.epmvGui.epmvGui object at 0x0D85FA08>>)
readMolecule WARNINGERROR: C:\Documents and Settings\Rémi\Bureau\glucose.pdb doesn't exists
menu 1052


Seems the plugin cannot find the molecule ?


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PostPosted: Thu Mar 29, 2012 7:24 pm 
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Joined: Wed Apr 22, 2009 2:08 am
Posts: 235
oh I see
look like it is the same problem with the plugin that wasn't starting.
It came from your username and the accent....
I will try to find a fix, in the meantime just put your data in C:\data or C:\Work or something like that and read the molecule from there.

Ludo


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PostPosted: Thu Mar 29, 2012 7:28 pm 
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Posts: 12
I tried to put the glucose.pdb file at /C: and the console show me this message :


C:\Documents and Settings\R魩\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\MGLToolsPckgs
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x0D855580>> ignored
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x0D855580>> ignored
execute
try to restore
None
<module 'c4d' (built-in)>
Resource file used to customize PMV: C:\Documents and Settings\R魩\.mgltools\latest\Pmv\_pmvrc
[(0.375, 0.5, 1.0), (0.93700000000000006, 0.0, 0.5), (1.0, 1.0, 0.0), (1.0, 1.0, 1.0)]
ERROR *********************************************
Traceback (most recent call last):
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\ViewerFramework\VF.py", line 898, in tryto
result = command( *args, **kw )
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\ViewerFramework\basicCommand.py", line 338, in doit
self.vf.addCommand( d['cmd'], d['name'], d['gui'])
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\ViewerFramework\VF.py", line 1288, in addCommand
command.onAddCmdToViewer()
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\Pmv\coarseMolSurfaceCommands.py", line 89, in onAddCmdToViewer
from DejaVu.VisionInterface.GeometryNodes import ConnectedComponents
File "C:\Documents and Settings\Ré­©\Application Data\MAXON\cinema 4d_34A33228\plugins\ePMV\mgl32\/MGLToolsPckgs\DejaVu\VisionInterface\GeometryNodes.py", line 34, in <module>
from NetworkEditor.items import NetworkNode
ImportError: No module named NetworkEditor.items
WARNING: dependency check failed for command APBSVolumeRender
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x16366558>> ignored
Exception AttributeError: "BooleanVar instance has no attribute '_tk'" in <bound method BooleanVar.__del__ of <Tkinter.BooleanVar instance at 0x16622FD0>> ignored
[(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), (0.9499999999999999
, 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), (0.94
99999999999996, 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), (0.9769999999999
998, 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, 0.664000000
0000003), (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), (0.699999999999999
6, 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), (0.69999999999999996, 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.
0000000000000001, 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, 0.299999
9999999999, 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, 0.93700000000000
06), (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, 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)]
[(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)]
[(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)]
[(0.0, 0.0, 1.0), (0.0, 1.0, 0.0), (1.0, 0.0, 0.0), (0.0, 1.0, 1.0), (1.0, 1.0, 0.0), (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)]
[(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)]
noModeller
noAutoFill
noARViewer
no pymol
no prody
[(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)]
('action ', 'Browse', <bound method epmvGui.browsePDB of <ePMV.epmvGui.epmvGui object at 0x0D85FA08>>)
<Protein instance> glucose with 1 MolKit.protein.Chain
0
('glucose', <Protein instance> glucose with 1 MolKit.protein.Chain)
('ok sel', 24)
no secondary structure set for chain: !
menu 1056


I tried another .pdb file (http://dl.dropbox.com/u/33321865/amylase.pdb) and this one works fine !!!!
This is great ! I hope you will able to solve the glucose.pdb problem and i will be happy :)

Thank you for spending time for me.

Romain


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PostPosted: Thu Mar 29, 2012 8:32 pm 
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Joined: Wed Apr 22, 2009 2:08 am
Posts: 235
you are welcome.

I don't see anything wrong with the glucose.pdb in your log. Glucose is a sugar, not a protein so there is no ribbon representation for it.
so load glucose.pdb and click Atom representation or Ball and stick representation or surface.

Ludo


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