Re: [PyMOL] apbs error (Error in background function)
Dear Thomas, thank you a lot for your quick reply. Just to help the users that might find these posts in the future; the path in my case was: /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py and the plugin settings look like this: ... # Global config variables # # To change the default locations, change these to something like # APBS_BINARY_LOCATION = '/opt/bin/' # APBS_BINARY_LOCATION = '/usr/bin/apbs/' APBS_WEB_LOCATION = None # corresponding environment variable: APBS_WEB_DIR APBS_PSIZE_LOCATION = '/usr/share/pdb2pqr/src/' APBS_PDB2PQR_LOCATION = '/usr/share/pdb2pqr/' TEMPORARY_FILE_DIR = tempfile.gettempdir() # corresponding environment variable: TEMP ... Kind regards, Matic Kisovec On 30. 01. 2015 21:21, Thomas Holder wrote: 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.simailto: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.simailto: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 PluginAPBS 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! attachment: matic_kisovec.vcf-- Dive
Re: [PyMOL] apbs error (Error in background function)
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 PluginAPBS 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
Re: [PyMOL] apbs error (Error in background function)
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.simailto: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 PluginAPBS 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! attachment: matic_kisovec.vcf-- 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
Re: [PyMOL] apbs error (Error in background function)
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 PluginAPBS 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! attachment: matic_kisovec.vcf-- 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
Re: [PyMOL] apbs error (Error in background function)
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 PluginAPBS 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
Re: [PyMOL] apbs error (Error in background function)
Hi, I think this is a known bug: http://sourceforge.net/p/pymolapbsplugin/bugs/1/ There is a fix mentioned but it involves patching the source code for the plugin, which worked for me but is somewhat involved. However it might help you find a solution or lead someone else to suggest something simpler that might work. Best wishes, Jens From: #DE FALCO JR LOUIS# [defa0...@e.ntu.edu.sg] Sent: 01 September 2014 01:54 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] apbs error (Error in background function) 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! -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ 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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ 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
