I seem to remember pmw opportunistically links to blt if it is present, but
builds without complaint if it is not. fink policy (as far as I understand it)
is to have everyone's pwm (or any package) build the same way, so at some point
I suggested making blt a dependency for pwm.
As for the fix on OS X, it is a one line change, so we can just make it on the
fly if you don't want to mess with the code.
On Dec 9, 2009, at 12:14 PM, Michael Lerner wrote:
> I don't call blt directly from my plugin. In fact, I don't plot anything in
> the plugin, so unless Pmw automatically makes some blt calls for me, the
> plugin is probably blt-free.
>
> I haven't used pynmr before but it looks like you have to either compile
> something or get a precompiled binary from the web. I'd rather stick with
> pure python for the APBS Tools plugin.
>
> It looks to me like the plugin is closing PyMOL rather than crashing it when
> I make the suggested changes under Ubuntu.
>
> -michael
>
> On Wed, Dec 9, 2009 at 12:05 PM, Jack Howarth <howa...@bromo.med.uc.edu>wrote:
>
>> Michael,
>> Do you know if the APBS Tools plugin uses blt? I have working under
>> the assumption that these problems are a manifestation of breakage in
>> the existing blt 2.4z. Have you consider changing ABPS Tools to
>> function more like pynmr (ie open its own window instead of a dialog)?
>> I don't think I've ever seen pynmr crash pymol.
>> Jack
>>
>> On Wed, Dec 09, 2009 at 11:14:08AM -0500, Michael Lerner wrote:
>>> Hi,
>>>
>>> When I try that on my Ubuntu image, it makes it so that quitting the
>> plugin
>>> causes PyMOL to quit.
>>>
>>> I don't really know much about tk. If there's a standard way to open /
>>> destroy the plugin, I'd be glad to change things around. As far as I
>> know,
>>> the relevant bits are
>>>
>>> def __init__(self,app):
>>> self.parent = app.root
>>>
>>> # Create the dialog.
>>> self.dialog = Pmw.Dialog(self.parent,
>>> buttons = ('Register APBS Use',
>> 'Register
>>> PDB2PQR Use', 'Set grid', 'Run APBS', 'Exit APBS tools'),
>>> title = 'PyMOL APBS Tools',
>>> command = self.execute)
>>> self.dialog.protocol('WM_DELETE_WINDOW',self.quit)
>>> self.dialog.withdraw()
>>> Pmw.setbusycursorattributes(self.dialog.component('hull'))
>>> ...
>>> self.showAppModal()
>>>
>>> def showAppModal(self):
>>> #self.dialog.activate(geometry = 'centerscreenfirst', globalMode
>> =
>>> 'nograb')
>>> #self.dialog.activate(geometry = 'centerscreenalways', globalMode
>> =
>>> 'nograb')
>>> #self.dialog.activate(geometry = 'centerscreenfirst')
>>> self.dialog.show()
>>>
>>> def execute(self, result, refocus=True):
>>> if result == 'Register APBS Use':
>>> ...
>>> else:
>>> #
>>> # Doing it this way takes care of clicking on the x in the
>> top
>>> of the
>>> # window, which as result set to None.
>>> #
>>> if __name__ == '__main__':
>>> #
>>> # dies with traceback, but who cares
>>> #
>>> self.parent.destroy()
>>> else:
>>> #self.dialog.deactivate(result)
>>> global APBS_BINARY_LOCATION, APBS_PSIZE_LOCATION
>>> APBS_BINARY_LOCATION = self.binary.getvalue()
>>> APBS_PSIZE_LOCATION = self.psize.getvalue()
>>> #self.dialog.withdraw()
>>> #self.dialog.destroy() # stops CPU hogging, perhaps fixes
>>> Ubuntu bug MGL
>>> self.quit()
>>> def quit(self):
>>> self.dialog.quit()
>>> self.parent.quit()
>>> #self.dialog.withdraw()
>>> #self.dialog.destroy()
>>>
>>>
>>> by the way, we've started a google wave about the plugin. I can add any
>> of
>>> you that want to be on it.
>>>
>>> -michael
>>>
>>> On Sat, Dec 5, 2009 at 12:02 AM, William G. Scott <
>>> wgsc...@chemistry.ucsc.edu> wrote:
>>>
>>>> Hi Jack:
>>>>
>>>> Again, many thanks. It has been a busy day so I didn't get a chance to
>> try
>>>> this until just now, but it fixed this highly annoying problem
>> immediately.
>>>>
>>>> I'll pass it along upstream.
>>>>
>>>> All the best,
>>>>
>>>> Bill
>>>>
>>>>
>>>> On Dec 4, 2009, at 8:25 AM, Jack Howarth wrote:
>>>>
>>>>> Bill,
>>>>> Looking through the changes in the abps_tools.py script from
>>>>> pymol 1.r1 to the current 1.2r2, I believe I've found the offending
>>>>> code. If I revert the change...
>>>>>
>>>>> --- modules/pmg_tk/startup/apbs_tools.py.broken 2009-12-04
>>>> 11:11:03.000000000 -0500
>>>>> +++ modules/pmg_tk/startup/apbs_tools.py 2009-12-04
>>>> 11:18:08.000000000 -0500
>>>>> @@ -1124,7 +1124,7 @@
>>>>> self.showAppModal()
>>>>>
>>>>> def showAppModal(self):
>>>>> - self.dialog.activate(geometry = 'centerscreenfirst',
>> globalMode
>>>> = 'nograb')
>>>>> + #self.dialog.activate(geometry = 'centerscreenfirst',
>> globalMode
>>>> = 'nograb')
>>>>> self.dialog.show()
>>>>> #self.dialog.activate(geometry = 'centerscreenalways')
>>>>>
>>>>> I find that the use of the ABPS tools window no longer nukes the use
>> of
>>>> the main tk
>>>>> interface menus afterwards. You may want to update the current
>> pymol-py
>>>> package with
>>>>> that change. I haven't tested it yet but this might also solve the
>> same
>>>> issue with
>>>>> pymol-py and the current x86_64 blt package.
>>>>> Jack
>>>>
>>>>
>>>
>>>
>>> --
>>> Michael Lerner, Ph.D.
>>> IRTA Postdoctoral Fellow
>>> Laboratory of Computational Biology NIH/NHLBI
>>> 5635 Fishers Lane, Room T909, MSC 9314
>>> Rockville, MD 20852 (UPS/FedEx/Reality)
>>> Bethesda MD 20892-9314 (USPS)
>>
>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
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