Re: [PyMOL] which code actually executes to load axplor file? Debugstatements not executing.
Hi Mike, I guess you are on Linux with Open-Source PyMOL, right? Can you send me the xplor file that causes PyMOL to segfault? From your backtrace it looks like the problem is related to crystal symmetry information. If you want to load some format which is not yet supported by PyMOL, the easiest solution is to convert it to some already supported format on the fly and feed that to PyMOL, if possible. Cheers, Thomas Mike Marchywka wrote, On 01/02/13 17:01: I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the problem but can't get my debug statements to execute. The only thing that greps for xplor is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol nothing seems to change. Is this the right code? I also wanted to add a loader for other formats of density or vector fields and maybe do some rendering (I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ 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] which code actually executes to load axplor file? Debugstatements not executing.
Thanks but it looks like I am ok now ( aside from orignally posting this on the wrong list LOL). My python build still hangs and has problems with the list area on right but the configure/make build process works fine and I could find the problem. Generally error checking is the last thing ayone wants to do and the positions sensitive fields are a big problem to find from a segfault. I think this is the 5..0.2 open source version. In any case, I wanted to allow for input of some custom file formats and maybe integrate with some of my old code and it now looks like I can do that. Would be happy to contribute at some point if I get something that works LOL. Thanks. Date: Thu, 3 Jan 2013 12:32:01 +0100 From: thomas.hol...@schrodinger.com To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] which code actually executes to load axplor file? Debugstatements not executing. Hi Mike, I guess you are on Linux with Open-Source PyMOL, right? Can you send me the xplor file that causes PyMOL to segfault? From your backtrace it looks like the problem is related to crystal symmetry information. If you want to load some format which is not yet supported by PyMOL, the easiest solution is to convert it to some already supported format on the fly and feed that to PyMOL, if possible. Cheers, Thomas Mike Marchywka wrote, On 01/02/13 17:01: I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the problem but can't get my debug statements to execute. The only thing that greps for xplor is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol nothing seems to change. Is this the right code? I also wanted to add a loader for other formats of density or vector fields and maybe do some rendering (I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ 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 -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ 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] which code actually executes to load axplor file? Debugstatements not executing.
never mind, it looks like the name case changes and opening in GDB gave me a bt, fwiw, presumably I can figure this out now... PyMOLcmd.load_raw(content, 'xplor', 'map',quiet=0) ObjectMapLoadXPLOR: Loading... Program received signal SIGSEGV, Segmentation fault. transform33f3f (m1=0xffc0ffc00044, m2=0x7fffa070, m3=0x7fffa080) at Vector.c:677 677 m3[0] = m1[0] * m2r0 + m1[1] * m2r1 + m1[2] * m2r2; (gdb) bt #0 transform33f3f (m1=0xffc0ffc00044, m2=0x7fffa070, m3=0x7fffa080) at Vector.c:677 #1 0x75761fdd in ObjectMapXPLORStrToMap (I=0x1dbf320, XPLORStr=optimized out, state=optimized out, quiet=0) at ObjectMap.c:3204 #2 0x7576b838 in ObjectMapReadXPLORStr (quiet=0, state=-1, XPLORStr=0x7fffeb685034 \n 4 !NTITLE\n line 2 desc\n line 3 desc\n line 4 desc\n line 5 desc\n 080 0 080 160 0 160 080 0 080 \n 0.85336E+02 0.85336E+02 0.75650E+02 0.9E+02 0.9E..., I=0x1dbf320, G=0xeb1300) at ObjectMap.c:4474 #3 ObjectMapLoadXPLOR (G=0xeb1300, obj=0x0, fname=optimized out, state=-1, is_file=0, quiet=0) at ObjectMap.c:5541 #4 0x7582c712 in ExecutiveLoad (G=0xeb1300, origObj=0x0, content=0x7fffeb685034 \n 4 !NTITLE\n line 2 desc\n line 3 desc\n line 4 desc\n line 5 desc\n 080 0 080 160 0 160 080 0 080 \n 0.85336E+02 0.85336E+02 0.75650E+02 0.9E+02 0.9E..., content_length=optimized out, content_format=26, object_name=0x7fffb210 map, state=-1, zoom=-1, discrete=0, finish=1, multiplex=-1, quiet=0, plugin=0x0) at Executive.c:3724 #5 0x7586a572 in CmdLoad (self=0x76177dc8, args=optimized out) at Cmd.c:7866 #6 0x004b66b9 in PyEval_EvalFrameEx () #7 0x004bcdbd in PyEval_EvalCodeEx () ---Type return to continue, or q return to quit--- #8 0x004b6c34 in PyEval_EvalFrameEx () #9 0x004bcdbd in PyEval_EvalCodeEx () #10 0x004bd892 in PyEval_EvalCode () #11 0x004dcd82 in ?? () #12 0x004dd7a5 in PyRun_StringFlags () #13 0x004bafc6 in PyEval_EvalFrameEx () #14 0x004bcdbd in PyEval_EvalCodeEx () #15 0x004b6c34 in PyEval_EvalFrameEx () #16 0x004bcdbd in PyEval_EvalCodeEx () #17 0x004b6c34 in PyEval_EvalFrameEx () #18 0x004bcdbd in PyEval_EvalCodeEx () #19 0x0044914f in ?? () #20 0x0042423c in ?? () #21 0x0042704d in PyObject_CallFunction () #22 0x756f7414 in PFlushFast (G=0xeb1300) at P.c:2665 #23 0x7586b616 in CmdFlushNow (self=0x76177dc8, args=optimized out) at Cmd.c:2931 #24 0x004b66b9 in PyEval_EvalFrameEx () #25 0x004bcdbd in PyEval_EvalCodeEx () #26 0x004b6c34 in PyEval_EvalFrameEx () #27 0x004bcdbd in PyEval_EvalCodeEx () #28 0x004b6c34 in PyEval_EvalFrameEx () #29 0x004bcdbd in PyEval_EvalCodeEx () ---Type return to continue, or q return to quit--- #30 0x0044914f in ?? () #31 0x0042423c in ?? () #32 0x004242e7 in ?? () #33 0x00427248 in PyObject_CallMethod () #34 0x7586fd96 in MainDrawLocked () at main.c:811 #35 0x7586ff53 in MainDraw () at main.c:1081 #36 0x747a0220 in ?? () from /usr/lib/libglut.so.3 #37 0x747a3939 in fgEnumWindows () from /usr/lib/libglut.so.3 #38 0x747a065a in glutMainLoopEvent () from /usr/lib/libglut.so.3 #39 0x747a0f65 in glutMainLoop () from /usr/lib/libglut.so.3 #40 0x75871504 in launch (options=0xeaf520, own_the_options=optimized out) at main.c:1955 #41 was_main () at main.c:2006 #42 0x75853dd4 in CmdRunPyMOL (self=0x76177df0, args=optimized out) at Cmd.c:4771 #43 0x004b66b9 in PyEval_EvalFrameEx () note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave message 989-348-4796 (P)- emergency From: marchy...@hotmail.com To: pymol-users@lists.sourceforge.net Date: Wed, 2 Jan 2013 11:01:52 -0500 Subject: [PyMOL] which code actually executes to load axplor file? Debugstatements not executing. I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the problem but can't get my debug statements to execute. The only thing that greps for xplor is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol nothing seems to change. Is this the right code? I also wanted to add a loader for other formats of density or vector fields and maybe do some rendering ( I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. -- Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery and much
