ADL: Autodock Tools stopped working after I registered.

Stefano Forli forli at scripps.edu
Thu Oct 11 18:04:20 PDT 2012


Rich,

Lion is not that new, but the version you are using has been released less than a month 
ago. I can't be sure about this, but since the error message at the end of your report 
points to OpenGL, I would suspect of the update (a backport of some of the changes that 
have been made in Mountain Lion?).

It is worth to try installing the new incoming stable version [1] of MGLTools and see if 
it helps.
Let me know,


Stefano


[1] http://mgltools.scripps.edu/downloads/mgltools-1-5-6-release-candidate

On 10/11/2012 12:16 PM, Richard Friedman wrote:
> 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 <mailto: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 <mailto: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 <mailto: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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