ADL: Autodock Tools stopped working after I registered.

Richard Friedman friedman at cancercenter.columbia.edu
Thu Oct 11 12:16:02 PDT 2012


Stefano,

	I have 10.7.5 "Lion". Lion has been around for a while.
Are you sure that the problem is with "Lion" and not the
new OS "Mountain Lion" whose bugs are still being worked out?

Thanks and best wishes,
Rich

On Oct 11, 2012, at 3:12 PM, Stefano Forli wrote:

> Rich,
> 
> the solution most likely to work would be to roll-back to the previous OS version. Since there was a change in the way OpenGL is handled, changing the MGLTools version is not going to help, unfortunately...
> 
> Stefano
> 
> On 10/11/2012 12:09 PM, Richard Friedman wrote:
>> Dear Stefano,
>> 
>> 	Would reinstalling adt help?
>> 	If so, is there anything I should do aside from throwing out the old version?
>> 	Was it caused by registering or was it incidental to registering?
>> 
>> Thanks and best wishes,
>> Rich
>> 
>> On Oct 11, 2012, at 3:03 PM, Stefano Forli wrote:
>> 
>>> Hi,
>>> 
>>> I'm sorry for the inconvenience. It is a known problem with the recent MacOS update (apparently, an issue with the OpenGL buffer accumulation), and we are working to fix it.
>>> 
>>> We'll keep you posted with updates.
>>> 
>>> Stefano
>>> 
>>> 
>>> On 10/11/2012 10:08 AM, Richard Friedman wrote:
>>>> Dear Autodock Tools list,
>>>> 
>>>> 	I am using mgltools_i86Darwin9_1.5.4 in MacOS 10.7.5.
>>>> I had neglected to register (I had registered previously on a
>>>> PC). Finally the program no longer gave me the "Remind me
>>>> later option). I registered. Then I no longer got the graphic
>>>> user interface. I received the following error message
>>>> in the python windowL
>>>> 
>>>> ccrfml1:~ friedman$ /Applications/mgltools_i86Darwin9_1.5.4/bin/adt ; exit;
>>>> Starting X11
>>>> setting PYTHONHOME environment
>>>> Run AutoDockTools from /Applications/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/AutoDockTools
>>>> Resource file used to customize PMV: /Users/friedman/.mgltools/1.5.4/Pmv/_pmvrc
>>>> Traceback (most recent call last):
>>>>   File "/Applications/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/AutoDockTools/__init__.py", line 373, in runADT
>>>>     title=title, withShell= not interactive, verbose=False)
>>>>   File "/Applications/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/Pmv/moleculeViewer.py", line 315, in __init__
>>>>     verbose=verbose, trapExceptions=trapExceptions)
>>>>   File "/Applications/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/ViewerFramework/VF.py", line 345, in __init__
>>>>     verbose=verbose)
>>>>   File "/Applications/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/ViewerFramework/VFGUI.py", line 277, in __init__
>>>>     cnf = {"addScenarioButton": False})
>>>>   File "/Applications/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/DejaVu/Viewer.py", line 587, in __init__
>>>>     c = apply(Viewer.AddCamera, (self, master, screenName,classCamera), kw)
>>>>   File "/Applications/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/DejaVu/Viewer.py", line 278, in AddCamera
>>>>     c = apply( classCamera, (master, screenName, self, len(self.cameras)), kw)
>>>>   File "/Applications/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/DejaVu/Camera.py", line 4806, in __init__
>>>>     check, cnf), **kw)
>>>>   File "/Applications/mgltools_i86Darwin9_1.5.4/MGLToolsPckgs/DejaVu/Camera.py", line 1603, in __init__
>>>>     Tkinter.Widget.__init__(self, self.frame, 'togl', cnf, kw)
>>>>   File "/mgl/python/releases/i86Darwin9/python2.5/lib/python2.5/lib-tk/Tkinter.py", line 1930, in __init__
>>>>     (widgetName, self._w) + extra + self._options(cnf))
>>>> TclError: Togl: couldn't get visual
>>>> hit enter to continue
>>>> 
>>>> I restarted the Mac but still had the same problem.
>>>> 
>>>> Is there a way I can solve this problem without reinstalling?
>>>> Should I reinstall mgl-tools?
>>>> Is there anything I should do aside from throwing out the old mglt-tools too prepare for the new version?
>>>> 
>>>> Thanks and best wishes,
>>>> Rich
>>>> Richard A. Friedman, PhD
>>>> Associate Research Scientist,
>>>> Biomedical Informatics Shared Resource
>>>> Herbert Irving Comprehensive Cancer Center (HICCC)
>>>> Lecturer,
>>>> Department of Biomedical Informatics (DBMI)
>>>> Educational Coordinator,
>>>> Center for Computational Biology and Bioinformatics (C2B2)/
>>>> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
>>>> Room 824
>>>> Irving Cancer Research Center
>>>> Columbia University
>>>> 1130 St. Nicholas Ave
>>>> New York, NY 10032
>>>> (212)851-4765 (voice)
>>>> friedman at cancercenter.columbia.edu
>>>> http://cancercenter.columbia.edu/~friedman/
>>>> 
>>>> In memoriam, Ray Bradbury
>>>> 
>>>> ________________________________________________
>>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>> 
>>> --
>>> Stefano Forli, PhD
>>> 
>>> Staff Scientist
>>> Molecular Graphics Laboratory
>>> Dept. Molecular Biology,  MB-112
>>> The Scripps Research Institute
>>> 10550  North Torrey Pines Road
>>> La Jolla,  CA 92037-1000,  USA.
>>> 
>>>    tel: (858) 784-2055
>>>    fax: (858) 784-2860
>>>    email: forli at scripps.edu
>>>    http://www.scripps.edu/~forli/
>> 
> 
> -- 
> Stefano Forli, PhD
> 
> Staff Scientist
> Molecular Graphics Laboratory
> Dept. Molecular Biology,  MB-112
> The Scripps Research Institute
> 10550  North Torrey Pines Road
> La Jolla,  CA 92037-1000,  USA.
> 
>    tel: (858) 784-2055
>    fax: (858) 784-2860
>    email: forli at scripps.edu
>    http://www.scripps.edu/~forli/



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