Re: [PyMOL] regarding APBS tools in PyMOL
Hi Vaheh, my recollection is a bit hazy, but I remember having some issues with the distributed APBS version earlier this year. Try downloading the latest APBS and run the plug-in generated input file using the latest version from the commandline. If that works you may have to swap the APBs binary or adjust the path to APBS accordingly. HTH Carsten From: Oganesyan, Vaheh [mailto:oganesy...@medimmune.com] Sent: Tuesday, April 22, 2014 9:45 AM To: pymol-users Subject: [PyMOL] regarding APBS tools in PyMOL Colleagues, The latest PyMOL version 1.7.0.3 looks like having issues with molecule size when APBS is being used. I’m loading whole molecule consisting of ~500 aa and APBS plugin after setting up the grid and after starting APBS run few seconds later opens a window with message: APBS stopped working. Close Program. If I load a portion of the molecule (and it doesn’t matter which, but should be less than 200 aa) then it works fine. It is being run on Intel Core i7, 64-bit with 8 GB RAM. Did anyone see such behavior? Regards, Vaheh 8-5851 To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Dynoplot from the command line
Hi,
After installing Dynoplot I was able to start it via the plugins menu
(which works fine), but when I try starting it via the command line it
throws an error (please see the log file).
Eventually I'd like to use Dynoplot in combination with "Monitor file
continuously" one to visualize the output from the structure
calculation on the fly.
Thank you,
Vitaly
PyMOL>fetch 2kb7
CmdLoad: ".\2kb7.pdb" loaded as "2kb7".
PyMOL>rama 2kb7
Traceback (most recent call last):
File "C:\Python26\lib\site-packages\pymol\parser.py", line 254, in parse
self.result=apply(layer.kw[0],layer.args,layer.kw_args)
File "C:\Python26\lib\site-packages\pmg_tk\startup\dynoplot.py", line 366, in
rama
dyno = DynoRamaObject(sel, name, symbols, int(state))
File "C:\Python26\lib\site-packages\pmg_tk\startup\dynoplot.py", line 272, in
__init__
rootframe = Pmw.MegaToplevel(pmgapp.root)
File "C:\Python26\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 980,
in __init__
MegaArchetype.__init__(self, parent, Tkinter.Toplevel)
File "C:\Python26\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 354,
in __init__
hullClass, (parent,))
File "C:\Python26\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 526,
in createcomponent
widget = apply(widgetClass, widgetArgs, kw)
File "C:\Python26\lib\lib-tk\Tkinter.py", line 1975, in __init__
BaseWidget.__init__(self, master, 'toplevel', cnf, {}, extra)
File "C:\Python26\lib\lib-tk\Tkinter.py", line 1932, in __init__
(widgetName, self._w) + extra + self._options(cnf))
TclError: out of stack space (infinite loop?)
--
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Re: [PyMOL] Detecting Plugins menu
I just found the pymol._ext_gui property, which seems to be None if X11 is off and a positive number if X11 is present. Seeing as it's a private variable, is it ok to use this to check for X11 presence? -Spencer On Thu, Apr 17, 2014 at 10:21 AM, Spencer Bliven wrote: > Here's what I'm currently using. It seems to work so far. Looking through > the PyMol binary I see about 50 possible names though, so it would be nice > if there were a built-in way to detect X11. > > def hasTk(): > """ Make an educated guess as to whether Tk is installed, > hopefully without triggering any installation on Macs > """ > hasTk = True > if sys.platform=="darwin": #Mac > # Hack: check the path for entries containing 'X11' > hasTk = any([ "X11" in p.upper() for p in sys.path]) > > if hasTk: > try: > import Tkinter > except ImportError: > hasTk = False > > return hasTk > > > On Mon, Apr 14, 2014 at 10:46 AM, Spencer Bliven wrote: > >> I'm working on a plugin with a command line interface and a light-weight >> tk interface through the plugins menu. This works fine on Linux, Windows, >> and open-source Mac builds, but not on MacPyMol.app. Importing Tkinter >> causes PyMol to quit with a prompt to install X11 (but not an ImportError, >> as far as I can tell). If X11 is installed there are no errors, but there >> is not a plugins menu, so I'd rather not bother loading and initializing >> the Tk interface to the plugin. >> >> How can I detect whether Tk is available? >> >> I can think of two approaches, but haven't figured out the correct >> commands for either. (1) Check the name that pymol was started with. >> "MacPyMol.app" does not have Tk, while "PyMOLX11Hybrid.app" does. I'm not >> sure how to get the name (maybe could be guessed from sys.path?), and I >> know there are a lot more variants than those two available. (2) Check for >> the existence of the plugins menu. But this would have to be done without >> importing Tk and triggering the X11 check. >> >> Is there a simple way to do this I'm overlooking? >> >> Thanks, >> -Spencer >> > > -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] regarding APBS tools in PyMOL
Colleagues, The latest PyMOL version 1.7.0.3 looks like having issues with molecule size when APBS is being used. I’m loading whole molecule consisting of ~500 aa and APBS plugin after setting up the grid and after starting APBS run few seconds later opens a window with message: APBS stopped working. Close Program. If I load a portion of the molecule (and it doesn’t matter which, but should be less than 200 aa) then it works fine. It is being run on Intel Core i7, 64-bit with 8 GB RAM. Did anyone see such behavior? Regards, Vaheh 8-5851 To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
