[PyMOL] Pymol, calculate enclosed volume of map
Hi, I have a volumetric map from an EM reconstruction I loaded into pymol and contoured at 4sigma (it went through the normal statistical averaging and normalization in pymol). I'd like to calculate the volume enclosed by the 4sigma contour, so that I can calculate an estimated mass. Does anyone have a script with that functionality? I'd rather not have to fire up chimera to do this as it's buggy on my computer. Ian - Ian Berke, PhD Associate Research Scientist, Modis Lab Department of Molecular Biophysics and Biochemistry Yale University 266 Whitney Ave, Bass 431 New Haven, CT 06520 (203) 432-4414 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://ad.doubleclick.net/clk;258768047;13503038;j? http://info.appdynamics.com/FreeJavaPerformanceDownload.html___ 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] Graphical Problems
I have this problem when I run pymol using the Intel driver on my Ubuntu 11.10 64bit machine. However, if I fire it up using the nvidia driver, I have no issues and it's very smooth. As someone else mentioned, this is likely due to the poor quality of Intel Sandy Bridge graphics chips. Here are my cards: Intel mobile - i915 driver Nvidia geforce gt 520m - nvidia-280.13-0ubuntu6 driver I use ironhide to run the nvidia card for graphics intensive programs Ian - Ian Berke, PhD Associate Research Scientist, Modis Lab Department of Molecular Biophysics and Biochemistry Yale University 266 Whitney Ave, Bass 431 New Haven, CT 06520 (203) 432-4414 Message: 6 Date: Wed, 7 Dec 2011 19:15:28 +0100 From: Julian Zachmann frankjulian.zachm...@uab.cat Subject: [PyMOL] Graphical Problems To: pymol-users@lists.sourceforge.net Message-ID: cahctmqsod9mu4mnum+pdzy_t1q2mxv2bwjuwf9ggv2xqn2d...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear Pymol-Users, I have a rather strange error. I can open pymol without having any problems or warnings. But when I'm looking at a protein then - especially when it is in cartoon mode, and even more when i move it around a lot - it is getting more and more blurry and it seems as if there are many small black spots on my protein. When I have more proteins aligned in different colors then I also see spots in the different colors on the protein. Has this problem occured to anyone else before? Does anyone know a solution to this problem? My pymol version is PyMOL 1.4.1, I'm running it on Ubuntu 11.10 64bit, and my graphical card is Intel Corporation 2nd Generation Core Processor Family. Best Regards, Julian -- next part -- An HTML attachment was scrubbed... -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/___ 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 HelpAbout. 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]
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 war...@delsci.com 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 HelpAbout. 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
Re: [PyMOL] Vacuum Electrostatics
Problem solved... next time I'll do a completely clean install. Sorry for the needless email. Ian On Mon, Jul 27, 2009 at 11:08 AM, Ian Berke ian.be...@yale.edu wrote: Hi, I'm getting this error still using a self-compiled version from the latest SVN and python 2.6.2. The error is: Alter-Error: Aborting on error. Assignment may be incomplete. File string, line 1 formal_charge=0;flags=flags0x-8388609 In a previous post it was reported to be fixed. Is anyone still having this issue? Thanks, Ian Mark, Should be fixed now (in rev 3720). Cheers, Wawrren -Original Message- From: Mark Wehner [mailto:mark.weh...@ru...] Sent: Monday, May 11, 2009 12:11 PM To: pymol-us...@li... Subject: [PyMOL] Vacuum electrostatics Hi everyone, in the newer version of pymol I realized it is not possible to generate vacuum electrostatics, there's an error while assigning the formal charges. The error message is: Alter-Error: Aborting on error. Assignment may be incomplete. File string, line 1 formal_charge=0;flags=flags0x-8388609 I build the source code (rev 3719) using Python 2.6.2. Is anyone experiencing similar problems at the moment? Mark -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list pymol-us...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users -- ___ 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
