[PyMOL] Loading PDB Files does not work with Linux
Hi all, I can't get the functions to load pdb-data from the internet to work under Linux. Neither "fetch" nor "load http://..."; nor the plugin remote_pdb_load.py will work (connection error - please check your internet access). Under windows at least the load... method and the plugin are operable, the fetch method does not work either. The familiar plugin ProxyConfig.py also is of no use. The Pymol versions are 1.0 and 1.2r1. We have to use a http-proxy, but the proxy-url and -port are present in the environment variable http_proxy. I would really like to use Linux, so, do you have any hints? How should I setup pymol as to use the proxy? Regards, Joachim -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf___ 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] Viewport dimensions query
Hi, Does anyone know how to get a hold of the viewport dimensions from within a script? I vaguely remember some posts about this subject, but could not find anything in my archive. Thanks Carsten -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf___ 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] Viewport dimensions query
Hi Carsten, Is this what you are looking for? http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html Best regards, Folmer Fredslund 2009/9/24 Schubert, Carsten [PRDUS] : > Hi, > > Does anyone know how to get a hold of the viewport dimensions from within a > script? I vaguely remember some posts about this subject, but could not find > anything in my archive. > > Thanks > > Carsten > > -- > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9-12, 2009. Register now! > http://p.sf.net/sfu/devconf > ___ > 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 > -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf ___ 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] Viewport dimensions query
Yep, thanks Folmer > -Original Message- > From: Folmer Fredslund [mailto:folm...@gmail.com] > Sent: Thursday, September 24, 2009 9:33 AM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Viewport dimensions query > > Hi Carsten, > > Is this what you are looking for? > http://www.mail-archive.com/pymol- > us...@lists.sourceforge.net/msg05888.html > > Best regards, > Folmer Fredslund > > 2009/9/24 Schubert, Carsten [PRDUS] : > > Hi, > > > > Does anyone know how to get a hold of the viewport dimensions from > within a > > script? I vaguely remember some posts about this subject, but could > not find > > anything in my archive. > > > > Thanks > > > > Carsten > > > > - > - > > Come build with us! The BlackBerry® Developer Conference in SF, > CA > > is the only developer event you need to attend this year. Jumpstart > your > > developing skills, take BlackBerry mobile applications to market and > stay > > ahead of the curve. Join us from November 9-12, 2009. Register > now! > > http://p.sf.net/sfu/devconf > > ___ > > 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- > us...@lists.sourceforge.net > > > > --- > --- > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9-12, 2009. Register > now! > http://p.sf.net/sfu/devconf > ___ > 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 -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf ___ 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] Loading PDB Files does not work with Linux
Joachim, PyMOL relies entirely upon Python's built-in proxy support (via urllib), so if you can get a Python script configured to work properly through your proxy, then PyMOL should work as well. http://www.python.org/doc/2.5.2/lib/module-urllib.html Cheers, Warren From: greipel.joac...@mh-hannover.de [mailto:greipel.joac...@mh-hannover.de] Sent: Thursday, September 24, 2009 5:51 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Loading PDB Files does not work with Linux Hi all, I can't get the functions to load pdb-data from the internet to work under Linux. Neither "fetch" nor "load http://..."; nor the plugin remote_pdb_load.py will work (connection error - please check your internet access). Under windows at least the load... method and the plugin are operable, the fetch method does not work either. The familiar plugin ProxyConfig.py also is of no use. The Pymol versions are 1.0 and 1.2r1. We have to use a http-proxy, but the proxy-url and -port are present in the environment variable http_proxy. I would really like to use Linux, so, do you have any hints? How should I setup pymol as to use the proxy? Regards, Joachim -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf___ 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] Pymol segmentation fault
Hi, I'm having an issue trying to run various plugins in pymol (apbs and autodock). Whenever I select a button that should bring up a file browser to choose a file (e.g. "Choose Externally generated pqr" in apbs) Pymol exits with: Segmentation fault (core dumped). Same thing happens when I go to Help>About. I can open and save files normally, and just about everything else works. I've tried this in pymol 1.1r2pre, where I can at least get the apbs plugin window to open, as well as the 1.2 trunk from svn (downloaded and compiled last week) which just crashes when I try to open the apbs window (I can install autodock.py and the window opens, but it crashes when I try to choose the location of files). I'm guessing this is something to do with the gui and tcl/tk, but don't have any idea how to troubleshoot (see the catchsegv output below). I'm running Ubuntu 9.10 on x86_64 and have a GeForce 8400M GS/PCI/SSE2 with the proprietory nvidia driver 185.18.36. Does anyone have any thoughts? Here is the backtrace portion from catchsegv: Backtrace: /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0] /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839] /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f] /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b] /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b] /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9] /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f] /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859] /usr/lib/libtcl8.5.so.0[0x7f639777dee6] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f63977543b8] /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f6397710a5f] /usr/lib/libtcl8.5.so.0[0x7f63977926d1] /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209] /usr/lib/libtcl8.5.so.0[0x7f6397793192] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413] /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32] /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python[0x52bdf0] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python[0x4254ff] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623] /usr/bin/python[0x49c06f] /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python[0x52bdf0] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python[0x4254ff] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623] /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376] /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f63977543b8] /usr/lib/libtcl8.5.so.0[0x7f63977527b9] /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706] /usr/lib/libtk8.5.so.0[0x7f6397a556f6] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413] /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870] /usr/lib/libtcl8.5.so.0[0x7f639779668f] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f63977543b8] /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f6397710a5f] /usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90] /usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35] /usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0] /usr/lib/libtk8.5.so.0[0x7f6397a37b48] /usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f] /usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff] /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201] /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python[0x52beed] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python[0x52bdf0] /usr/bin/python(PyObject_Cal
Re: [PyMOL] Pymol segmentation fault
Ian, Based on that traceback, it looks like you have two conflicting versions of Tcl (8.4 as well as 8.5) linked against and running in the same process...that could be the source of the crash. Cheers, Warren From: Ian Berke [mailto:ian.be...@yale.edu] Sent: Thursday, September 24, 2009 11:26 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Pymol segmentation fault Hi, I'm having an issue trying to run various plugins in pymol (apbs and autodock). Whenever I select a button that should bring up a file browser to choose a file (e.g. "Choose Externally generated pqr" in apbs) Pymol exits with: Segmentation fault (core dumped). Same thing happens when I go to Help>About. I can open and save files normally, and just about everything else works. I've tried this in pymol 1.1r2pre, where I can at least get the apbs plugin window to open, as well as the 1.2 trunk from svn (downloaded and compiled last week) which just crashes when I try to open the apbs window (I can install autodock.py and the window opens, but it crashes when I try to choose the location of files). I'm guessing this is something to do with the gui and tcl/tk, but don't have any idea how to troubleshoot (see the catchsegv output below). I'm running Ubuntu 9.10 on x86_64 and have a GeForce 8400M GS/PCI/SSE2 with the proprietory nvidia driver 185.18.36. Does anyone have any thoughts? Here is the backtrace portion from catchsegv: Backtrace: /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0] /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839] /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f] /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b] /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b] /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9] /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f] /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859] /usr/lib/libtcl8.5.so.0[0x7f639777dee6] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f63977543b8] /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f6397710a5f] /usr/lib/libtcl8.5.so.0[0x7f63977926d1] /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209] /usr/lib/libtcl8.5.so.0[0x7f6397793192] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413] /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32] /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python[0x52bdf0] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python[0x4254ff] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623] /usr/bin/python[0x49c06f] /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d] /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] /usr/bin/python[0x52bdf0] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python[0x4254ff] /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623] /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376] /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f63977543b8] /usr/lib/libtcl8.5.so.0[0x7f63977527b9] /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706] /usr/lib/libtk8.5.so.0[0x7f6397a556f6] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413] /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870] /usr/lib/libtcl8.5.so.0[0x7f639779668f] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f63977543b8] /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0] /usr/lib/libtcl8.5.so.0[0x7f63977102f1] /usr/lib/libtcl8.5.so.0[0x7f6397710a5f] /usr/lib/libtk8.5.so
Re: [PyMOL] Pymol segmentation fault
> Does anyone have any thoughts?
Two things to try that may or may not help:
1. Check if the problem persists when running pymol in single-threaded
mode ("cmd.set('max_threads',1)"). libpthread in the trace might
indicate that one of the libraries is having issues with multiple threads.
2. On Kubuntu 8.04.3 LTS x64, I can't reproduce the problem with 1.2
from svn trunk. This is using Tcl/Tk 8.4 (with pymol using it's own
source build of python 2.4.2, which may or may not be relevant); so
installing Tcl/Tk 8.4 instead of 8.5 (source or binary) might help
resolve the problem, or at least eliminate one possible source.
Pete
> Here is the backtrace portion from catchsegv:
> Backtrace:
> /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0]
> /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839]
> /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f]
> /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b]
> /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b]
> /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9]
> /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f]
> /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859]
> /usr/lib/libtcl8.5.so.0[0x7f639777dee6]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
> /usr/lib/libtcl8.5.so.0[0x7f63977926d1]
> /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209]
> /usr/lib/libtcl8.5.so.0[0x7f6397793192]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/bin/python[0x49c06f]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376]
> /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0[0x7f63977527b9]
> /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706]
> /usr/lib/libtk8.5.so.0[0x7f6397a556f6]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413]
> /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870]
> /usr/lib/libtcl8.5.so.0[0x7f639779668f]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f63977543b8]
> /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0]
> /usr/lib/libtcl8.5.so.0[0x7f63977102f1]
> /usr/lib/libtcl8.5.so.0[0x7f6397710a5f]
> /usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90]
> /usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35]
> /usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0]
> /usr/lib/libtk8.5.so.0[0x7f6397a37b48]
> /usr/lib/libtcl8.5.so.0(Tcl_ServiceEvent+0x7f)[0x7f639778764f]
> /usr/lib/libtcl8.5.so.0(Tcl_DoOneEvent+0x8f)[0x7f63977878ff]
> /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f639805f201]
> /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52beed]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_EvalFrameEx+0x3921)[0x4a0f31]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47]
> /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0]
> /usr/bin/python[0x52bdf0]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python[0x4254ff]
> /usr/bin/python(PyObject_Call+0x47)[0x41d6e7]
> /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623]
> /usr/bin/python[0x4d0c4d]
> /lib/libpthr
Re: [PyMOL] Pymol segmentation fault
Thank you! This was indeed the case. I have no idea why tcl/tk 8.4 was installed with 8.5 at the same time. Removing 8.4 and using 8.5 seems to have fixed the problem. Ian On Thu, Sep 24, 2009 at 2:38 PM, Warren DeLano wrote: > Ian, > > Based on that traceback, it looks like you have two conflicting versions of > Tcl (8.4 as well as 8.5) linked against and running in the same > process...that could be the source of the crash. > > Cheers, > Warren > > -- > *From:* Ian Berke [mailto:ian.be...@yale.edu] > *Sent:* Thursday, September 24, 2009 11:26 AM > *To:* pymol-users@lists.sourceforge.net > *Subject:* [PyMOL] Pymol segmentation fault > > Hi, > > I'm having an issue trying to run various plugins in pymol (apbs and > autodock). Whenever I select a button that should bring up a file browser > to choose a file (e.g. "Choose Externally generated pqr" in apbs) Pymol > exits with: Segmentation fault (core dumped). Same thing happens when I go > to Help>About. I can open and save files normally, and just about > everything else works. > > I've tried this in pymol 1.1r2pre, where I can at least get the apbs plugin > window to open, as well as the 1.2 trunk from svn (downloaded and compiled > last week) which just crashes when I try to open the apbs window (I can > install autodock.py and the window opens, but it crashes when I try to > choose the location of files). I'm guessing this is something to do with > the gui and tcl/tk, but don't have any idea how to troubleshoot (see the > catchsegv output below). I'm running Ubuntu 9.10 on x86_64 and have a > GeForce 8400M GS/PCI/SSE2 with the proprietory nvidia driver 185.18.36. > > Does anyone have any thoughts? > > Here is the backtrace portion from catchsegv: > Backtrace: > /usr/lib/libtcl8.5.so.0[0x7f63977b3eb0] > /usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f6397761839] > /usr/lib/libtcl8.4.so.0(Tcl_FindNamespaceVar+0xff)[0x7f6391d8352f] > /usr/lib/libtcl8.4.so.0(TclLookupSimpleVar+0xfb)[0x7f6391d9bf0b] > /usr/lib/libtcl8.4.so.0(TclLookupVar+0xab)[0x7f6391d9b70b] > /usr/lib/libtcl8.4.so.0(Tcl_SetVar2Ex+0x59)[0x7f6391d9c8e9] > /usr/lib/libtcl8.4.so.0(Tcl_SetVar2+0x4f)[0x7f6391d9c80f] > /usr/lib/libBLT.2.4.so.8.4(Blt_Init+0x169)[0x7f6392311859] > /usr/lib/libtcl8.5.so.0[0x7f639777dee6] > /usr/lib/libtcl8.5.so.0[0x7f63977102f1] > /usr/lib/libtcl8.5.so.0[0x7f63977543b8] > /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0] > /usr/lib/libtcl8.5.so.0[0x7f63977102f1] > /usr/lib/libtcl8.5.so.0[0x7f6397710a5f] > /usr/lib/libtcl8.5.so.0[0x7f63977926d1] > /usr/lib/libtcl8.5.so.0(Tcl_PkgRequireProc+0x9)[0x7f6397792209] > /usr/lib/libtcl8.5.so.0[0x7f6397793192] > /usr/lib/libtcl8.5.so.0[0x7f63977102f1] > /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413] > /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398063a32] > /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d] > /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] > /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] > /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] > /usr/bin/python(PyEval_EvalFrameEx+0x5837)[0x4a2e47] > /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] > /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f] > /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] > /usr/bin/python(PyEval_EvalFrameEx+0x4e4f)[0x4a245f] > /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] > /usr/bin/python[0x52bdf0] > /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] > /usr/bin/python[0x4254ff] > /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] > /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623] > /usr/bin/python[0x49c06f] > /usr/bin/python(PyEval_EvalFrameEx+0x52fd)[0x4a290d] > /usr/bin/python(PyEval_EvalCodeEx+0x860)[0x4a40e0] > /usr/bin/python[0x52bdf0] > /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] > /usr/bin/python[0x4254ff] > /usr/bin/python(PyObject_Call+0x47)[0x41d6e7] > /usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x49c623] > /usr/lib/python2.6/lib-dynload/_tkinter.so[0x7f6398061376] > /usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f639770e80f] > /usr/lib/libtcl8.5.so.0[0x7f63977102f1] > /usr/lib/libtcl8.5.so.0[0x7f63977543b8] > /usr/lib/libtcl8.5.so.0[0x7f63977527b9] > /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x196)[0x7f6397711706] > /usr/lib/libtk8.5.so.0[0x7f6397a556f6] > /usr/lib/libtcl8.5.so.0[0x7f63977102f1] > /usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f6397710413] > /usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x300)[0x7f6397711870] > /usr/lib/libtcl8.5.so.0[0x7f639779668f] > /usr/lib/libtcl8.5.so.0[0x7f63977102f1] > /usr/lib/libtcl8.5.so.0[0x7f63977543b8] > /usr/lib/libtcl8.5.so.0(TclObjInterpProcCore+0x110)[0x7f6397796ed0] > /usr/lib/libtcl8.5.so.0[0x7f63977102f1] > /usr/lib/libtcl8.5.so.0[0x7f6397710a5f] > /usr/lib/libtk8.5.so.0(Tk_BindEvent+0x890)[0x7f6397a29c90] > /usr/lib/libtk8.5.so.0(TkBindEventProc+0x185)[0x7f6397a2fa35] > /usr/lib/libtk8.5.so.0(Tk_HandleEvent+0x6c0)[0x7f6397a374c0] > /usr/lib/libtk8.5.so.0[
