I have two boxes. On one of them pymol-plugins-ezviz work as expected, but on the other one I get the error below when I invoke it. The configuration of both boxes is almost the same, apart from the kernel config and the graphic card drivers: === Error: 1 <type 'exceptions.AttributeError'> Exception in Tk callback Function: <function <lambda> at 0x2ec3668> (type: <type 'function'>) Args: () Traceback (innermost last): File "/usr/lib64/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/lib64/python2.6/site-packages/pmg_tk/startup/ez-viz.py", line 19, in <lambda> command = lambda s=self : PGUI(s)) File "/usr/lib64/python2.6/site-packages/pmg_tk/startup/ez-viz.py", line 2002, in __init__ self.getPdb() File "/usr/lib64/python2.6/site-packages/pmg_tk/startup/ez-viz.py", line 1523, in getPdb self.update(self.p) File "/usr/lib64/python2.6/site-packages/pmg_tk/startup/ez-viz.py", line 2273, in update self.advancedSelection.setitems(chainList) <type 'exceptions.AttributeError'>: PGUI instance has no attribute 'advancedSelection' === Then, when working for instance with the 1pkz.pdb file, all of the presets work except "Polarity", which fails this way: === Error: 2 QuietException Exception in Tk callback Function: <bound method PGUI.view_polarity of <pmg_tk.startup.ez-viz.PGUI instance at 0x2b80a70>> (type: <type 'instancemethod'>) Args: () Traceback (innermost last): File "/usr/lib64/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/lib64/python2.6/site-packages/pmg_tk/startup/ez-viz.py", line 565, in view_polarity cmd.show('surface','hydrophobic') File "/usr/lib64/python2.6/site-packages/pymol/viewing.py", line 595, in show if _self._raising(r,_self): raise QuietException QuietException: <pymol.parsing.QuietException instance at 0x3637bd8> === I have tcl/tk emerged with threads support on both machines: === $ eix -I tcl [I] dev-lang/tcl Available versions: (0) 8.4.15 8.4.18 8.4.18[2] ~8.4.19 ~8.4.19[2] 8.5.7 8.5.7[2] ~8.5.8 ~8.5.8[2] ~8.6_beta1[1] ~8.6_beta1[3] (8.4) ~8.4.19[4] (8.5) ~8.5.6[4] (8.6) ~8.6_beta1[4] {debug lib32 +tclcompat threads} Installed versions: 8.5.7(03:58:33 03/04/10)(threads -debug) Homepage: http://www.tcl.tk/ Description: Tool Command Language ... $ eix -I tk ... [I] dev-lang/tk Available versions: (0) 8.4.15-r1 8.4.18 8.4.18[10] 8.4.18-r1 8.4.18-r1[10] ~8.4.19-r1 ~8.4.19-r1[10] 8.5.7 8.5.7[10] ~8.5.7-r1 ~8.5.7-r1[10] ~8.5.8 ~8.5.8[10] ~8.6_beta1[3] ~8.6_beta1[16] (8.4) ~8.4.19-r1[17] (8.5) ~8.5.6[17] (8.6) ~8.6_beta1[17] {debug lib32 threads truetype} Installed versions: 8.5.7(07:37:14 03/04/10)(threads truetype -debug) Homepage: http://www.tcl.tk/ Description: Tk Widget Set ... === What can I check to find the difference between the working and the non-working box? Reproducible: Always
I can reproduce it here. How do the arches are different?
(In reply to comment #1) > I can reproduce it here. I'm not sure if I have to be glad about that ;-) > How do the arches are different? Both are amd64. Last week I did twice an "emerge -e world" on the ez-viz faulty machine, just in case, to no avail. Thanks for investigating the issue. I'm completely clueless and have no python/tcl/tk knowledge.
(In reply to comment #0) > On one of them pymol-plugins-ezviz work as expected I correct myself. It turns out if you launch the script without previously loading a pdb file, the Tk errors don't show up until you select "Polarity". Any other "preset" option just does nothing without a pdb loaded. Sorry for the confusion.
I think it is because the objects like "hydrophobic" aren't created correctly at startup. But it takes me some more time to figure out why. Did you tested it with different pymol versions?
No, I just tested it with the latest portage version: === $ eix -I pymol [I] sci-chemistry/pymol Available versions: 0.99_rc10 (~)0.99_rc10[1] (~)0.99_rc10[2] (~)1.0-r1 1.2.1 (~)1.2.2 (~)1.2.2-r2 (~)1.2.2-r4 (~)1.2.3-r1 [M](~)9999[1] [M](~)9999[2] {apbs numpy shaders vmd} Installed versions: 1.2.3-r1(02:43:10 04/04/10)(apbs numpy shaders vmd) Homepage: http://pymol.sourceforge.net/ Description: A Python-extensible molecular graphics system. ...
I will remove the plugin again, because all functionality of EZ-WIZ is included in the PROMOL Ez-Viz module. PLease try that one.
(In reply to comment #6) > I will remove the plugin again, because all functionality of EZ-WIZ is included > in the PROMOL Ez-Viz module. PLease try that one. > No, please, don't do that! Even if "Polarity" fails, the other presets are pretty useful. With the EZ-Viz module inside ProMOL you can't get the stand-alone EZ-VIZ preset effects that easily. Besides, there are options in ProMOL's EZ-Viz module which don't seem to work, also. For instance, "Preset Views" -> "Preset Movies" -> "Surface to Stick" or "Surface to Carbon".
I will move into the science overlay.
Thanks :)
