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ZareliMan
PostPosted: Wed Oct 07, 2009 5:33 am 
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Hello
I´ve been using autodocktools (1.5.2) since last year under windows xp and ubuntu. After a hardware upgrade I installed windows vista and debian and I installed the latest version (1.5.4) and it used to run perfectly under linux x86 or x86_64 and windows 32bit or 64 bit. The software actually works under any environment.
2 days ago I tried to run ADT under debian as always, I got the splash screen and froze at 100%, displaying an IndexError on the command screen... weird I thought, so I reinstalled the software from installer, then from tar.gz, then from repositories but none of them would work. I also tried the 1.5.6 and 1.6.0 builds without any luck. I thought it was a linux's issue so I rebooted under vista 64bit. Now this is very weird, under vista I got the exact same error on the console (except for locations like "Program Files"):

Code:
F:\Users\ZareliMan>set MGLPYTHONPATH=F:\Program Files (x86)\MGLTools 1.5.6

F:\Users\ZareliMan>"F:\Python25\python.exe" "F:\Program Files (x86)\MGLTools 1.5
.6\MGLToolsPckgs\AutoDockTools\bin\runAdt.py"
Run ADT from  F:\Program Files (x86)\MGLTools 1.5.6\MGLToolsPckgs\AutoDockTools
Resource file used to customize PMV: F:\Users\ZareliMan\.mgltools\1.5.6\Pmv\_pmv
rc
Traceback (most recent call last):
  File "F:\Program Files (x86)\MGLTools 1.5.6\MGLToolsPckgs\AutoDockTools\__init
__.py", line 432, in runADT
    title=title, withShell= not interactive, verbose=False, gui=gui)
  File "F:\Program Files (x86)\MGLTools 1.5.6\MGLToolsPckgs\Pmv\moleculeViewer.p
y", line 316, in __init__
    verbose=verbose, trapExceptions=trapExceptions)
  File "F:\Program Files (x86)\MGLTools 1.5.6\MGLToolsPckgs\ViewerFramework\VF.p
y", line 345, in __init__
    verbose=verbose)
  File "F:\Program Files (x86)\MGLTools 1.5.6\MGLToolsPckgs\ViewerFramework\VFGU
I.py", line 287, in __init__
    verbose=verbose,guiMaster=VIEWER_root,)
  File "F:\Program Files (x86)\MGLTools 1.5.6\MGLToolsPckgs\DejaVu\Viewer.py", l
ine 656, in __init__
    cp = ClippingPlane(self.rootObject, i, self)
  File "F:\Program Files (x86)\MGLTools 1.5.6\MGLToolsPckgs\DejaVu\Clip.py", lin
e 42, in __init__
    self.id = self.clipPlaneNames[num]
IndexError: list index out of range
hit enter to continue


I can´t figure out what happened, it´s very unlikely that´s related to the OS since It stopped working on both linux and windows at the same time ! I didn´t change my hardware configuration or anything, it just stopped working from one day to another...

Any suggestions ?
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ZareliMan
PostPosted: Thu Oct 08, 2009 12:30 am 
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I found out what the problem was... I updated ATI´s linux drivers and vista upgraded them automatically for me to the 9.9 version. I rolled back to 9.8 drivers and MGLTools worked once again.
ATI´s latest drivers (Catalyst 9.9) are NOT compatible with MGLTools, but 9.8 and earlier work... Maybe I should email them about this issue.
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sargis
PostPosted: Thu Oct 08, 2009 3:24 am 
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Thank you for the update. Your message is very much appreciated.

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urcindalo
PostPosted: Mon Feb 08, 2010 8:11 am 
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MGLTools 1.5.4 do not launch either on a 64bit gentoo laptop with ati-drivers 9.11. I see the same error:

Code:
$ runAdt                                                                                                                         
Run AutoDockTools from /usr/lib64/python2.6/site-packages/AutoDockTools                                                                         

Welcome to Python Molecule Viewer!
Visit http://mgltools.scripps.edu/documentation to read latest documentation.

Resource file used to customize PMV: /home/user/.mgltools/1.5.4/Pmv/_pmvrc

>>> Traceback (most recent call last):                                       
  File "/usr/lib64/python2.6/site-packages/AutoDockTools/__init__.py", line 373, in runADT
    title=title, withShell= not interactive, verbose=False)                               
  File "/usr/lib64/python2.6/site-packages/Pmv/moleculeViewer.py", line 315, in __init__
    verbose=verbose, trapExceptions=trapExceptions)
  File "/usr/lib64/python2.6/site-packages/ViewerFramework/VF.py", line 345, in __init__
    verbose=verbose)
  File "/usr/lib64/python2.6/site-packages/ViewerFramework/VFGUI.py", line 270, in __init__
    cnf = {"addScenarioButton": False})
  File "/usr/lib64/python2.6/site-packages/DejaVu/Viewer.py", line 675, in __init__
    cp = ClippingPlane(self.rootObject, i, self)
  File "/usr/lib64/python2.6/site-packages/DejaVu/Clip.py", line 42, in __init__
    self.id = self.clipPlaneNames[num]
IndexError: list index out of range
hit enter to continue


I also have a 64bit gentoo desktop, the configuration of which is exactly like the laptop's, but with an old Nvidia card. On my desktop computer I have no problem whatsoever launching mgltools 1.5.4.
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mflashbr
PostPosted: Sat Jun 19, 2010 2:34 am 
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FYI, the cause is a bug in the ATI driver, which in my machine incorrectly returns the number of clipping planes as 8, but actually only provides 6 (as defined by the OpenGL spec). Hence the index out of bounds error.

A simple fix is to edit the MGLToolsPckgs/DejaVu/Viewer.py and insert the following if command:

Code:
... (line 601) ...
# Find out how many clipping planes
maxClipP = int(GL.glGetDoublev(GL.GL_MAX_CLIP_PLANES)[0])
if(maxClipP > 6):
      maxClipP = 6 # the driver can't provide more than 6 clipping planes   
...


I'm running Ubuntu 10.04 with flgrx version 8.723.1-0ubuntu3.

Hope this helps someone.
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hsp1985
PostPosted: Sun Jul 18, 2010 9:28 pm 
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I've the same problem with ATI drivers on my ubuntu 10.04. :?
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magrathea
PostPosted: Thu Jul 29, 2010 7:47 am 
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Thank you mflashbr.
I tried for months to get ADT work after driver update.
The editing to Viewer.py file that you suggested worked fine.
All the best.

I'm on XP pro Service pack 3
ATI 4600 HD - Driver Packaging Version - 8.753-100706m-102491C-ATI
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leandrohornos
PostPosted: Tue Jul 26, 2011 12:23 am 
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mflashbr wrote:
FYI, the cause is a bug in the ATI driver, which in my machine incorrectly returns the number of clipping planes as 8, but actually only provides 6 (as defined by the OpenGL spec). Hence the index out of bounds error.

A simple fix is to edit the MGLToolsPckgs/DejaVu/Viewer.py and insert the following if command:

Code:
... (line 601) ...
# Find out how many clipping planes
maxClipP = int(GL.glGetDoublev(GL.GL_MAX_CLIP_PLANES)[0])
if(maxClipP > 6):
      maxClipP = 6 # the driver can't provide more than 6 clipping planes   
...


I'm running Ubuntu 10.04 with flgrx version 8.723.1-0ubuntu3.

Hope this helps someone.



This used to work for me on Kubuntu 10.04 with an ATI HD 4670 Card but now on Kubuntu 11.04 it doesn't work anymore.
By trial and error I've found that editing another line in the MGLToolsPckgs/DejaVu/Viewer.py file solves the problem:

where it says

Code:
 self.activeClippingPlanes = 0 # number of active clipping planes


change 0 to 6 and it should work.
At the end you'll end up with something like this:

Code:
 -------------- line 617----------------       
# for each geometry on a given side
   self.maxClipP = maxClipP
   self.clipP = []
        self.activeClippingPlanes = 6 # number of active clipping planes



Hope this helps someone.

Good luck!
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