Re: [PyMOL] Segmentation fault

Thanks for the tips Thomas. I will try and let you know. João On Tue, Apr 11, 2017 at 9:12 PM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi João, > > Before diving into the hassle of installing additional compilers (which > probably won't make a difference) I recommend to get famil

Re: [PyMOL] Segmentation fault

Hi João, Before diving into the hassle of installing additional compilers (which probably won't make a difference) I recommend to get familiar with a debugger like gdb and obtain a stack trace of the crash. To compile PyMOL with debug symbols, do export DEBUG=1 before running setup.py. Then r

Re: [PyMOL] Segmentation fault

Thanks for the feedback, Folmer! I am using CentOS. I already used --use-msgpackc=no and it did not improve. gcc --version gives me 4.8.5 (I cannot update more). Do you think it would be worth it to install gcc 4.9? On the install page there was said that a regression to 4.4 could work, but I don’

Re: [PyMOL] Segmentation fault

Hi João, On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9 and "--use-msgpackc=no" I get a working pymol with revision 4170. Have you tried creating a new user and test pymol from that account? That should help you identify if it is solely a problem with your own accoun

Re: [PyMOL] Segmentation fault

Nobody experiencing the same issues? Any tips on what I may be doing wrong on the installation? João On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas wrote: > Dear all, > > I started experiencing segmentation fault on a pymol that I had installed > through the omnia channel on conda. > > Then, I

Re: [PyMOL] Segmentation fault when I tried to load a pdb file

Hi Beibei, Googling for "gallium llvmpipe" suggests that your system is running on the wrong graphics driver: https://www.google.com/search?q=gallium+llvmpipe People solved this by reinstalling the correct driver and/or fixing permission problems. Cheers, Thomas On 14 Oct 2015, at 17:05, b

Re: [PyMOL] Segmentation Fault

Hi Narin - Hope you don't mind me reviving an old thread, but I just ran into this same problem trying to build Pymol from source (and using fink for the dependencies) on my laptop. What solved it for me was the following: fink remove libpng16 libpng16-shlibs I guess pymol was trying to use l

Re: [PyMOL] Segmentation fault while cmd.read_pdbstr on MacOS

Hi Dominik, We've fixed this and pushed the changes to the open-source (revision 3993). Cheers, -- Jason On Fri, Mar 2, 2012 at 1:07 PM, Jason Vertrees wrote: > Hi Dominik, > > This looks like a bug. We're looking into it. > > Cheers, > > -- Jason > > On Thu, Mar 1, 2012 at 11:35 AM, Dominik G

Re: [PyMOL] Segmentation fault while cmd.read_pdbstr on MacOS

Hi Dominik, This looks like a bug. We're looking into it. Cheers, -- Jason On Thu, Mar 1, 2012 at 11:35 AM, Dominik G wrote: > Hi pymolers, > > I attempt to send a structure from a program to PyMol, which doesn't work. > After some time I've managed to extract the smallest data making the cras

Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

Hi Jason, My version of Ubuntu was 11.04 and the graphics card is the Intel integrated card. I don't know what's the problem, but I upgrade to 11.10 today. It works now. Thank you very much for your reply. Cheers, Tao On Tue, Oct 18, 2011 at 10:10 AM, Jason Vertrees wrote: > Hi Tao, > > What ve

Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

Hi Tao, What version of Ubuntu are you running? I'm running 11.04 (and recently upgraded to 11.10). It works fine for me. What video card do you have? How did you install? Cheers, -- Jason On Mon, Oct 17, 2011 at 6:08 PM, Tao-wei Huang wrote: > Hi all, > > I have problems with starting pymol i

Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

On Tue, Oct 18, 2011 at 12:08 AM, Tao-wei Huang wrote: > Hi all, > > I have problems with starting pymol in ubuntu. When I started it from > terminal, I just received the error message: Segmentation fault. I > tried googling pymol segmentation fault, but I don't find effective > information to fix

Re: [PyMOL] Segmentation fault while starting Pymol in ubuntu 11

What version do you have installed? Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/10/17 Tao-wei Huang > Hi all, > > I have problems with starting pymol in ubuntu. When I started it from > terminal, I just re

Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

Hey :) After removing the svn source copy, as well as the pymol version installed globally through apt-get, followed by downloading the source anew and compiling, I ended up with a working copy. Apparently there were some version conflicts... The take home message: clean up before cooking :) Che

Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

Hi Tsjerk, > Intel GMA 950 card, 945GSE chipset, check :( The mobile Intel video drivers have been problematic for us and quite a few other graphics software groups. Some of our users have been reporting success after they upgrade their drivers. For others though, it doesn't help. On Windows t

Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

Hey Jason, Intel GMA 950 card, 945GSE chipset, check :( So this is a known problem, and is there a workaround? Do you need additional information from my side? Cheers, Tsjerk On Mon, Apr 11, 2011 at 6:06 PM, Jason Vertrees wrote: > Hi, > >> The problem did not occur on another machine (Intel

Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

Hi, > The problem did not occur on another machine (Intel Core i7, 64bit), > running Ubuntu 10.10. > On my EeePC loading a python CGO file worked fine, while loading an > empty PDB file segfaulted. So it seems to be related to loading the > coordinates, not to the displaying. Is anyone else havin

Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

Hi, The problem did not occur on another machine (Intel Core i7, 64bit), running Ubuntu 10.10. On my EeePC loading a python CGO file worked fine, while loading an empty PDB file segfaulted. So it seems to be related to loading the coordinates, not to the displaying. Cheers, Tsjerk On Mon, Apr

Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

Hi Jason & Tsjerk ... Just for the info that I just downloaded, compiled and tried it on OpenSuse 11.4 and it ran without any problems: PyMOL>load ../../3lzt.pdb HEADERHYDROLASE 23-MAR-97 3LZT TITLE REFINEMENT OF TRICLINIC LYSOZYME AT ATOMIC RESOLUTION COM

Re: [PyMOL] Segmentation fault rendering CGO object with all_states one

Hi Tsjerk, Thanks for bringing this to my attention. The fix (revision 3929) has been pushed to the open-source SVN on SourceForge. You can try out the following code segments to verify: ### # TEST 1 from pymol import cmd from pymol.cgo import * from pymol.vfont import plain

Re: [PyMOL] Segmentation fault rendering CGO object with all_states one

Hi Tsjerk, That is indeed a bug. I'll look into it and post the changes back to SVN when it's fixed. Cheers, -- Jason On Mon, Jan 3, 2011 at 11:34 AM, Tsjerk Wassenaar wrote: > Hi Jason, > > It appears that Pymol segfaults rendering when a cgo object spans > multiple states, and all_states is

Re: [PyMOL] Segmentation fault r3910 on linux with Python 2.5/2.6 and tcl/tk 8.5.5 and 8.6b1.

Hi Edward, Choosing the correct Tcl/Tk version is necessary, and sometimes easy to overlook. Glad to hear it works. Cheers, -- Jason On Thu, Jun 10, 2010 at 2:01 PM, Edward d'Auvergne wrote: > Hi, > > Sorry, this was not compiled properly!  catchsegv showed that tcl/tk > 8.6 was being used.  

Re: [PyMOL] segmentation fault -- fedora 13

The version that seg faults in fedora 13 is the edu build: *PyMOL 1.2edu1* (August 2009) Linux: pymol-1_2edu1-bin-linux-x86-centos45.tgz The fedora 13 rpm build does not segfault. I am really confused on the differences between the RPM and the official builds by PyMol via supscription. http:

Re: [PyMOL] Segmentation fault r3910 on linux with Python 2.5/2.6 and tcl/tk 8.5.5 and 8.6b1.

Hi, Sorry, this was not compiled properly! catchsegv showed that tcl/tk 8.6 was being used. Setting LD_LIBRARY_PATH for the alternative tcl/tk libraries for the Python and PyMOL compilation fixed the problem. The segfault is gone when using Python 2.5.5 with tcl/tk 8.5. It also works with Pyth

Re: [PyMOL] segmentation fault in 1.2r3pre 64-bit on linux

Hi Ben, A couple things come to mind: (1) Always use the latest "proven" NVidia drivers; 180.xx is not current. (2) Some RH versions use Tcl/Tk 8.4 over 8.5. Which is yours using? (3) Could you please send me the md5 sum for your copy? We should make sure it's not corrupted. Cheers, -- Jason

Re: [PyMOL] segmentation fault!

Hi, I can try to look into this, although I'm not sure what's causing it. Can you tell me - what version of PyMOL you have and how it was installed - what version of APBS you have and how it was installed - when exactly the segmentation fault happens (are you working with a particular PDB file

Re: [PyMOL] segmentation fault after switching mainwindow between visualisation and commandline

Am Dienstag, 21. November 2006 15:58 schrieb Christian Seifert: > $PYTHONPATH is not set on my machine. > > > > You wrote: > > Re: segmentation fault after switching mainwindow between > visualisation and commandline > From: Martin - 2006-11-13 05:15 > >... i had a similar Prob

Re: [PyMOL] segmentation fault after switching mainwindow between visualisation and commandline

$PYTHONPATH is not set on my machine. You wrote: Re: segmentation fault after switching mainwindow between visualisation and commandline From: Martin - 2006-11-13 05:15 ... i had a similar Problem this morning. What is your PYTHONPATH? For me, unsetting it solved

Re: [PyMOL] segmentation fault after switching mainwindow between visualisation and commandline

... i had a similar Problem this morning. What is your PYTHONPATH? For me, unsetting it solved the problems. Cheers Martin

Re: [PyMOL] Segmentation fault when selection is too large

Sebastien, Break it up over multiple selection statements which reuse the prior selection. For example, select mysel, resi 123+124+125 select mysel, mysel or resi 234+345+346 etc. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC