From: jp d <yo...@ya...> - 2014-02-11 19:52:16
|
hi, anyone else having trouble with the apbs plugin? i keep crashing as soon as i try to do anything. if i select 'Choose externally generated PQR' or 'run APBS' i get this In show error 1 alloc: invalid block: 0x2aaaac29fb78: 0 0 Abort this is with pymol 1.7 ubuntu 12.04 using 1FAS fetched from the pdb thanks jpd |
From: Schubert, C. [JRDUS] <CSC...@it...> - 2014-02-11 20:14:11
|
Hi jpd, try running APBS directly just using the .in file generated from a failed run. That may provide a clue as to where the problem is, i.e. within APBS itself or within the plugin. If it is APBS, which is throwing the error you may want to try to grab an updated version or the source code to compile yourself. HTH Carsten From: jp d [mailto:yo...@ya...] Sent: Tuesday, February 11, 2014 2:52 PM To: pym...@li... Subject: [PyMOL] apbs plugin hi, anyone else having trouble with the apbs plugin? i keep crashing as soon as i try to do anything. if i select 'Choose externally generated PQR' or 'run APBS' i get this In show error 1 alloc: invalid block: 0x2aaaac29fb78: 0 0 Abort this is with pymol 1.7 ubuntu 12.04 using 1FAS fetched from the pdb thanks jpd |
From: jp d <yo...@ya...> - 2014-02-11 21:21:34
|
hi, good idea, it runs from the command line after adding /pymol/ext/lib to my library path but the plugin still crashes. something is odd about my APBS plugin setup. if i even just click to change the file locations it crashes. the other plugins seem fine. thanks jpd ________________________________ From: "Schubert, Carsten [JRDUS]" <CSC...@it...> To: jp d <yo...@ya...>; "pym...@li..." <pym...@li...> Sent: Tuesday, February 11, 2014 12:14 PM Subject: RE: [PyMOL] apbs plugin Hi jpd, try running APBS directly just using the .in file generated from a failed run. That may provide a clue as to where the problem is, i.e. within APBS itself or within the plugin. If it is APBS, which is throwing the error you may want to try to grab an updated version or the source code to compile yourself. HTH Carsten From:jp d [mailto:yo...@ya...] Sent: Tuesday, February 11, 2014 2:52 PM To: pym...@li... Subject: [PyMOL] apbs plugin hi, anyone else having trouble with the apbs plugin? i keep crashing as soon as i try to do anything. if i select 'Choose externally generated PQR' or 'run APBS' i get this In show error 1 alloc: invalid block: 0x2aaaac29fb78: 0 0 Abort this is with pymol 1.7 ubuntu 12.04 using 1FAS fetched from the pdb thanks jpd |
From: Thomas H. <tho...@sc...> - 2014-02-12 18:35:56
|
Hi jpd, I can reproduce this, unfortunately. Thanks for reporting. It's indeed a problem with the GUI toolkit and not apbs itself. We are looking into it. Cheers, Thomas On 11 Feb 2014, at 16:21, jp d <yo...@ya...> wrote: > hi, > good idea, it runs from the command line after adding > /pymol/ext/lib to my library path > > but the plugin still crashes. > something is odd about my APBS plugin setup. > if i even just click to change the file locations > it crashes. > > the other plugins seem fine. > > thanks > jpd > > From: "Schubert, Carsten [JRDUS]" <CSC...@it...> > To: jp d <yo...@ya...>; "pym...@li..." <pym...@li...> > Sent: Tuesday, February 11, 2014 12:14 PM > Subject: RE: [PyMOL] apbs plugin > > Hi jpd, > > try running APBS directly just using the .in file generated from a failed run. That may provide a clue as to where the problem is, i.e. within APBS itself or within the plugin. If it is APBS, which is throwing the error you may want to try to grab an updated version or the source code to compile yourself. > > HTH > > Carsten > > From: jp d [mailto:yo...@ya...] > Sent: Tuesday, February 11, 2014 2:52 PM > To: pym...@li... > Subject: [PyMOL] apbs plugin > > hi, > anyone else having trouble with the apbs plugin? > i keep crashing as soon as i try to do anything. > if i select 'Choose externally generated PQR' > or 'run APBS' i get this > In show error 1 > alloc: invalid block: 0x2aaaac29fb78: 0 0 > Abort > > this is with pymol 1.7 > ubuntu 12.04 > using 1FAS fetched from the pdb > > thanks > jpd -- Thomas Holder PyMOL Developer Schrödinger, Inc. |
From: jp d <yo...@ya...> - 2014-02-12 19:16:56
|
hi, if i enable debugging i get a little more info get_default_location will search the following : ['/xtal/programs/pymol/ext', '/xtal/programs/pymol/ext/share/pdb2pqr', '/xtal/programs/pymol/ext/bin', '/sw/share/pdb2pqr', '/sw/share/apbs/tools/manip', '/sw/share/apbs-mpi-openmpi/tools/manip', '/sw/share/apbs-mpi-lammpi/tools/manip', '/usr/local/share/tools/manip', '/xtal/programs/3dna/x3dna-v2.1/bin', '/xtal/programs/xdsme-0.5beta1/bin/noarch', '/xtal/programs/cns_solve_1.21/intel-x86_64bit-linux/bin', '/xtal/programs/cns_solve_1.21/intel-x86_64bit-linux/utils', '/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/bin', '/home/donohue/bin', '/usr/local/sbin', '/usr/local/bin', '/usr/sbin', '/usr/bin', '/sbin', '/bin', '/usr/games', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] trying /xtal/programs/pymol/ext/pdb2pqr.py trying /xtal/programs/pymol/ext/pdb2pqr trying /xtal/programs/pymol/ext/share/pdb2pqr/pdb2pqr.py get_default_location will search the following : ['/tmp', '/tmp', '.'] get_default_location will search the following : ['/tmp', '/tmp', '.'] get_default_location will search the following : ['/tmp', '/tmp', '.'] get_default_location will search the following : ['/tmp', '/tmp', '.'] alloc: invalid block: 0x2aaaac29fb78: 0 0 Abort ________________________________ From: Thomas Holder <tho...@sc...> To: jp d <yo...@ya...> Cc: "Schubert, Carsten [JRDUS]" <CSC...@it...>; "pym...@li..." <pym...@li...> Sent: Wednesday, February 12, 2014 10:35 AM Subject: Re: [PyMOL] apbs plugin Hi jpd, I can reproduce this, unfortunately. Thanks for reporting. It's indeed a problem with the GUI toolkit and not apbs itself. We are looking into it. Cheers, Thomas On 11 Feb 2014, at 16:21, jp d <yo...@ya...> wrote: > hi, > good idea, it runs from the command line after adding > /pymol/ext/lib to my library path > > but the plugin still crashes. > something is odd about my APBS plugin setup. > if i even just click to change the file locations > it crashes. > > the other plugins seem fine. > > thanks > jpd > > From: "Schubert, Carsten [JRDUS]" <CSC...@it...> > To: jp d <yo...@ya...>; "pym...@li..." <pym...@li...> > Sent: Tuesday, February 11, 2014 12:14 PM > Subject: RE: [PyMOL] apbs plugin > > Hi jpd, > > try running APBS directly just using the .in file generated from a failed run. That may provide a clue as to where the problem is, i.e. within APBS itself or within the plugin. If it is APBS, which is throwing the error you may want to try to grab an updated version or the source code to compile yourself. > > HTH > > Carsten > > From: jp d [mailto:yo...@ya...] > Sent: Tuesday, February 11, 2014 2:52 PM > To: pym...@li... > Subject: [PyMOL] apbs plugin > > hi, > anyone else having trouble with the apbs plugin? > i keep crashing as soon as i try to do anything. > if i select 'Choose externally generated PQR' > or 'run APBS' i get this > In show error 1 > alloc: invalid block: 0x2aaaac29fb78: 0 0 > Abort > > this is with pymol 1.7 > ubuntu 12.04 > using 1FAS fetched from the pdb > > thanks > jpd -- Thomas Holder PyMOL Developer Schrödinger, Inc. |
From: jp d <yo...@ya...> - 2014-02-13 20:20:46
|
hi, more information: down in function askfilename if i change self.activate() to self.show() i can get the file dialogue to pop up but cant do anything with it. its also near where tabs and spaces start making for confusing indentation. that might be the source of the problem. ________________________________ From: jp d <yo...@ya...> To: Thomas Holder <tho...@sc...> Cc: "Schubert, Carsten [JRDUS]" <CSC...@it...>; "pym...@li..." <pym...@li...> Sent: Wednesday, February 12, 2014 11:16 AM Subject: Re: [PyMOL] apbs plugin hi, if i enable debugging i get a little more info get_default_location will search the following : ['/xtal/programs/pymol/ext', '/xtal/programs/pymol/ext/share/pdb2pqr', '/xtal/programs/pymol/ext/bin', '/sw/share/pdb2pqr', '/sw/share/apbs/tools/manip', '/sw/share/apbs-mpi-openmpi/tools/manip', '/sw/share/apbs-mpi-lammpi/tools/manip', '/usr/local/share/tools/manip', '/xtal/programs/3dna/x3dna-v2.1/bin', '/xtal/programs/xdsme-0.5beta1/bin/noarch', '/xtal/programs/cns_solve_1.21/intel-x86_64bit-linux/bin', '/xtal/programs/cns_solve_1.21/intel-x86_64bit-linux/utils', '/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/bin', '/home/donohue/bin', '/usr/local/sbin', '/usr/local/bin', '/usr/sbin', '/usr/bin', '/sbin', '/bin', '/usr/games', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] trying /xtal/programs/pymol/ext/pdb2pqr.py trying /xtal/programs/pymol/ext/pdb2pqr trying /xtal/programs/pymol/ext/share/pdb2pqr/pdb2pqr.py get_default_location will search the following : ['/tmp', '/tmp', '.'] get_default_location will search the following : ['/tmp', '/tmp', '.'] get_default_location will search the following : ['/tmp', '/tmp', '.'] get_default_location will search the following : ['/tmp', '/tmp', '.'] alloc: invalid block: 0x2aaaac29fb78: 0 0 Abort ________________________________ From: Thomas Holder <tho...@sc...> To: jp d <yo...@ya...> Cc: "Schubert, Carsten [JRDUS]" <CSC...@it...>; "pym...@li..." <pym...@li...> Sent: Wednesday, February 12, 2014 10:35 AM Subject: Re: [PyMOL] apbs plugin Hi jpd, I can reproduce this, unfortunately. Thanks for reporting. It's indeed a problem with the GUI toolkit and not apbs itself. We are looking into it. Cheers, Thomas On 11 Feb 2014, at 16:21, jp d <yo...@ya...> wrote: > hi, > good idea, it runs from the command line after adding > /pymol/ext/lib to my library path > > but the plugin still crashes. > something is odd about my APBS plugin setup. > if i even just click to change the file locations > it crashes. > > the other plugins seem fine. > > thanks > jpd > > From: "Schubert, Carsten [JRDUS]" <CSC...@it...> > To: jp d <yo...@ya...>; "pym...@li..." <pym...@li...> > Sent: Tuesday, February 11, 2014 12:14 PM > Subject: RE: [PyMOL] apbs plugin > > Hi jpd, > > try running APBS directly just using the .in file generated from a failed run. That may provide a clue as to where the problem is, i.e. within APBS itself or within the plugin. If it is APBS, which is throwing the error you may want to try to grab an updated version or the source code to compile yourself. > > HTH > > Carsten > > From: jp d [mailto:yo...@ya...] > Sent: Tuesday, February 11, 2014 2:52 PM > To: pym...@li... > Subject: [PyMOL] apbs plugin > > hi, > anyone else having trouble with the apbs plugin? > i keep crashing as soon as i try to do anything. > if i select 'Choose externally generated PQR' > or 'run APBS' i get this > In show error 1 > alloc: invalid block: 0x2aaaac29fb78: 0 0 > Abort > > this is with pymol 1.7 > ubuntu 12.04 > using 1FAS fetched from the pdb > > thanks > jpd -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |