Dear Matic, the only option to permanently store those paths is to edit the plugin file. Look for "apbs_tools.py" in the PyMOL installation directory and there for "Global config variables".
Cheers, Thomas On 30 Jan 2015, at 00:33, Matic Kisovec <matic.kiso...@ki.si> wrote: > Dear Thomas, > > thank you for your quick reply. > I can confirm that now APBS tools2.1 plugin inside Pymol 1.7.4 works as > expected. > > I do have one more issue. Every time I execute Pymol I get two lines saying: > Could not find default location for file: psize.py > Could not find default location for file: pdb2pqr.py > I manually set up the paths but they get lost when I exit pymol. > Is there a way to permanently store this information? > > Kind regards, > Matic > > On 28. 01. 2015 16:58, Thomas Holder wrote: >> Dear Matic, >> >> this was fixed for 1.7.4: >> https://sourceforge.net/p/pymol/code/4099/ >> >> >> Please install the latest version. >> >> Cheers, >> Thomas >> >> On 28 Jan 2015, at 10:04, Matic Kisovec >> <matic.kiso...@ki.si> >> wrote: >> >> >>> Dear Pymol users, >>> >>> I have recieved the same error as mentioned in the email ate bottom that >>> was sent by DE FALCO JR LOUIS in September 2014 to this list. There was one >>> reply that is a known bug and a link was provided. The bug was filed in >>> March 2013. >>> >>> The difference is this time this happened on Ubuntu 14.04.1 OS. So I tried >>> a quick and fresh install inside Virtualbox and after the OS installation >>> finished I installed Pymol and its dependencies. Pymol version in Ubuntu >>> repositories is 1.7.0. When I select Plugin>APBS Tools2.1 I get a popup >>> with the following error that is almost identical to the one from DE FALCO >>> JR LOUIS: >>> Error: 1 >>> <class '_tkinter.TclError'> Exception in Tk callback >>> Function: <function <lambda> at 0x7faa60852578> (type: <type 'function'>) >>> Args: () >>> Traceback (innermost last): >>> File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line >>> 1747, in __call__ >>> return apply(self.func, args) >>> File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", >>> line 314, in <lambda> >>> command = lambda s=self: APBSTools2(s)) >>> File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py", >>> line 680, in __init__ >>> group.pack(fill='both',expand=1, padx=4, pady=5) >>> File "<string>", line 1, in pack >>> None >>> File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1890, in pack_configure >>> + self._options(cnf, kw)) >>> <class '_tkinter.TclError'>: cannot use geometry manager pack inside >>> .140369735891136.140369735892288.140369735980600.140369614990728 which >>> already has slaves managed by grid >>> I am wondering though if this is some problem on my side since it has not >>> been mentioned very often online. That is why I tried a fresh installation >>> inside Virtualbox and the issue was the same. >>> >>> Any help would be greatly appreciated. >>> >>> Kind regards, >>> Matic >>> >>> >>> >>> Hello, >>> >>> I just updated PyMol Open Source to version 1.7.2.0-2 via the fink >>> package manager. Now, when I initiate the APBS Tools.1 plugin the >>> following error occurs: >>> >>> Error in background function >>> >>> Error: 1 >>> <class '_tkinter.TclError'> Exception in Tk callback >>> Function: <function <lambda> at 0x10cc75230> (type: <type 'function'>) >>> Args: () >>> Traceback (innermost last): >>> File "/sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line >>> 1753, in __call__ >>> return apply(self.func, args) >>> File "/sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line >>> 314, in <lambda> >>> command = lambda s=self: APBSTools2(s)) >>> File "/sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py", line >>> 680, in __init__ >>> group.pack(fill='both',expand=1, padx=4, pady=5) >>> File "<string>", line 1, in pack >>> None >>> File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure >>> + self._options(cnf, kw)) >>> <class '_tkinter.TclError'>: cannot use geometry manager pack inside >>> .4509565296.4509566808.4509809840.4510083120 which already has slaves >>> managed by grid >>> >>> I brought this to the attention of apbs developers who suggested I post >>> this error here as it seems related to PyMol and not apbs. Not a very >>> savvy user here so this may be entirely my fault. >>> >>> Thank you! -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ 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
