I just found that the packages have been updated and, indeed, molmol is now
working. Thank you, all. Very much appreciated.
all the best,
g
On Aug 13, 2011, at 6:21 PM, Jack Howarth wrote:
> On Sat, Aug 13, 2011 at 01:45:29PM -0700, Glenn Millhauser wrote:
>> I'd love to give it a try. What do I do with the code you have below?
>> G
>>
>
> Glenn,
> On Lion, the packaging for mesa-libglw and molmol on fink tracking should
> work...
>
> http://sourceforge.net/tracker/?func=detail&aid=3391210&group_id=17203&atid=414256
> http://sourceforge.net/tracker/?func=detail&aid=3391212&group_id=17203&atid=414256
>
> Jack
>
>> On Saturday, August 13, 2011, Jack Howarth <howa...@bromo.med.uc.edu> wrote:
>>> On Sat, Aug 13, 2011 at 12:22:14PM -0700, Glenn Millhauser wrote:
>>>> 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
>>>
>>> Glenn,
>>> Actually, I think I have a workaround...
>>>
>>> --- /sw/bin/molmol.sav 2011-08-13 16:32:28.000000000 -0400
>>> +++ /sw/bin/molmol 2011-08-13 16:38:14.000000000 -0400
>>> @@ -161,8 +161,8 @@
>>> esac
>>> fi
>>>
>>> -if [ "$input" = "-" -o -n "$nograph" ]; then
>>> +#if [ "$input" = "-" -o -n "$nograph" ]; then
>>> echo "LineBond solid 1 " >>| $startmacro ;
>> /sw/share/molmol/src/main/molmol $xopt
>>> -else
>>> - echo "LineBond solid 1 " >>| $startmacro ;
>> /sw/share/molmol/src/main/molmol $xopt < /dev/null
>>> -fi
>>> +#else
>>> +# echo "LineBond solid 1 " >>| $startmacro ;
>> /sw/share/molmol/src/main/molmol $xopt < /dev/null
>>> +#fi
>>>
>>> For some reason the extra redirection from /dev/null seems to break under
>> Lion.
>>> Jack
>>>
>>>>
>>>> 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 L. Millhauser
>> Chemistry
>> UCSC
>> voice (831) 459-2176
>> cell (831) 566-3337
>>
>> 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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