Okay -- I'll check in periodically. This is unfortunate. Molmol is dated, but
there are a few things that it does really well, much better than most of the
current software. Fingers crossed for a fix.
all the best,
g
On Aug 13, 2011, at 10:51 AM, Jack Howarth wrote:
> On Sat, Aug 13, 2011 at 10:37:54AM -0700, Glenn Millhauser wrote:
>> Thank you, Jack. So then even if I install Macports, molmol will not run --
>> am I right on this? I guess, then, molmol is dead for the time being. Is
>> there any way for me to follow the Xquartz progress to see when things are
>> updated, thus enabling molmol, once again? My understanding of all this
>> stuff is not deep -- I really appreciate the information/advice.
>> thanks,
>> glenn
>>
>
> Glenn,
> The Xquartz development mailing list is archived at
> http://lists.macosforge.org/pipermail/xquartz-dev/.
> The MacPorts xorg packages are more or less synchronized with those releases.
> In MacPorts, they build and link
> against those xorg packages in /opt/local but run with the Xserver from
> either the system X11 or Xquartz.
> I've opened https://svn.macports.org/ticket/30746 but wouldn't get my hopes
> up for a quick fix since we never
> determined what xorg change eliminated the previous instance of this widget
> issue in MacPorts. Also if it
> is a fixable flaw in X11/Xquartz, you'll have to wait for a fixed release of
> either the system X11 or Xquartz.
> Jack
>
>>
>> On Aug 13, 2011, at 10:02 AM, Jack Howarth wrote:
>>
>>> On Sat, Aug 13, 2011 at 09:49:09AM -0700, Glenn Millhauser wrote:
>>>> So does this mean that we have no chance of getting molmol running again?
>>>> Jack, if I understand correctly, you tried to build a fresh molmol in Lion
>>>> with the latest Fink distribution, but the windows still do not display
>>>> properly. Is there anything that you recommend that I try? If I
>>>> understand Alexander's suggestion, I could install the latest Fink and
>>>> then try "fink rebuild molmol." Any chance of that solving the problem?
>>>> thanks,
>>>> glenn
>>>
>>> Glenn,
>>> What is means is that the issue has to be punted to the Xquartz
>>> developers. This is one reason
>>> I ported molmol/pymol to MacPorts was so that those packages could be
>>> tested against the upcoming
>>> Xquartz releases (which appear in the form of their xorg related packages).
>>> Either the problem
>>> was previously fixed and then broken again or it just went latent for
>>> awhile. This was a major
>>> concern of mine about the absence of Xquartz support in fink (that we would
>>> be blindsided with
>>> X11 issues on new system releases that adopted the work from Xquartz).
>>> Jack
>>>
>>>>
>>>>
>>>> On Aug 13, 2011, at 7:54 AM, Jack Howarth wrote:
>>>>
>>>>> As far as I have been able to tell the breakage seems to be introduced
>>>>> with the
>>>>> new X11 in Lion. The molmol program built either under SL and run under
>>>>> Lion or
>>>>> built under Lion fails to display the widgets or menus in its windows.
>>>>> The current
>>>>> bahavior looks a lot like something we saw on MacPorts previously...
>>>>>
>>>>> https://trac.macports.org/ticket/21835
>>>>>
>>>>> Perhaps the problem resurfaced again. Unfortunately it was never
>>>>> determined exactly
>>>>> what change to the xorg packages solved the problem.
>>>>> Jack
>>>>>
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>>>>
>>>>
>>>> Glenn Millhauser
>>>> Department of Chemistry & Biochemistry
>>>> UC Santa Cruz
>>>> Santa Cruz, CA 95064
>>>>
>>>> 831 459 2176 voice
>>>> 831 459 2935 fax
>>>> 831 566 3337 cell
>>>>
>>>> gle...@ucsc.edu
>>>>
>>>> http://chemistry.ucsc.edu/~glennm
>>>>
>>>>
>>>>
>>>>
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>>
>>
>>
>> Glenn Millhauser
>> Department of Chemistry & Biochemistry
>> UC Santa Cruz
>> Santa Cruz, CA 95064
>>
>> 831 459 2176 voice
>> 831 459 2935 fax
>> 831 566 3337 cell
>>
>> gle...@ucsc.edu
>>
>> http://chemistry.ucsc.edu/~glennm
>>
>>
>>
>>
Glenn Millhauser
Department of Chemistry & Biochemistry
UC Santa Cruz
Santa Cruz, CA 95064
831 459 2176 voice
831 459 2935 fax
831 566 3337 cell
gle...@ucsc.edu
http://chemistry.ucsc.edu/~glennm
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