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

[PyMOL] Segmentation fault

Dear all, I started experiencing segmentation fault on a pymol that I had installed through the omnia channel on conda. Then, I decided to install from scratch using this recipe: https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN Still getting the segmentation fault, so may

[PyMOL] segmentation fault

Dear developer, I had this segmentation fault problem whenever using plugin like apbs or autodock etc. it crashes when I click button "APBS binary location" etc, Tried both pymol 1.7.4 and 1.8.0 and gave the same error. Any help would be greatly appreciated. Detected OpenGL version 2.0 or greater

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

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

HelloI just installed pymol on my machine (ubuntu 14; Graphics: Gallium 0.4 on llvmpipe): sudo apt-get install pymol. And I could open pymol, but when I tried to load a pdb file. It crashed and closed, and I got the following errorsF pymol: line 3: 17889 Segmentation fault.Could you help me to

[PyMOL] Segmentation fault with pymol2

Dear all, I have implemented a software in python/pyQT to draw chemical structure. For the visualisation it uses a pymol widget (using the pymol2 package). I haven't used it for a while (it was part of an old project), but today I noticed that it is no longer working. When I run the following code:

[PyMOL] Segmentation fault when using APBS Tool 2

The newest version of PyMOL (1.7.1.3) solves this problem, just to announce you to know that. Thank you. -- "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across

[PyMOL] Segmentation fault when using APBS Tool 2

Hi all, When I want to using the APBS Tool 2 to show the solvent accessible surface, pyMOL crashes and auto close, no matter the Solvent accessible surface and Color by potential on sol. acc. surf. are checked. The trace back is: Could not find pymol-generated.dx so searching for pymol- genera

[PyMOL] segmentation fault with pymol 1.6 (r4050)

Hi to everyone Recently moved to latest pymol (from subversion r4050) on linux (ubuntu 12.10). Installation was fine and could launch pymol successfully. Using builder crashes with a segmentation fault. Has anyone encountered this? Please give suggestions to overcome this issue. Thanks Best Rega

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

[PyMOL] Segmentation Fault

Hi all, I'm not very experienced with installing things from source, so you'll have to bear with me a bit here…. I'm trying to get pymol 1.6.0.0 working on my macbook (OS X 10.8.4). The install seems to go ok (home directory set to /sw) but when I try to launch pymol, it exits with this messag

[PyMOL] segmentation fault in Ubuntu12.10

Dear Sir, > When I load the map,big-sized map of virus, in pymol v1.5 > on my computer with 64bit ubuntu 12.10, the pymol run very slow and then > showed "segmentation fault". On my old computer with Ubuntu 9.10, the same > map can run very smooth. > > > Thank you Hong-Hsiang -

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

[PyMOL] Segmentation fault while cmd.read_pdbstr on MacOS

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 crash. So the segfault always happens when I do this: ~/bin/MacPyMOL.app/Contents/MacOS/MacPyMOL -p < incmd where the incmd file contains

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

> 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 this probl

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

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 this problem. If you have any idea or experience > about this, plea

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 effect

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

; terminal, I just received the error message: Segmentation fault. I > tried googling pymol segmentation fault, but I don't find effective > information to fix this problem. If you have any idea or experience > about this, please tell me. Thank yo

[PyMOL] Segmentation fault while starting Pymol in ubuntu 11

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 this problem. If you have any idea or experience about

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

[PyMOL] segmentation fault pymol 1.4 rev 3938

Hi Jason, I run into a segfault with Pymol 1.4 rev 3938 on my EEE PC, running Ubuntu 9.04. The segfault occurs when loading the PDB file. It happens regardless of the contents of the PDB file, but loading something with hetatms gives some insight in how far it goes: PyMOL>load ../../../3lzt.pdb H

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

[PyMOL] Segmentation fault rendering CGO object with all_states one

Hi Jason, It appears that Pymol segfaults rendering when a cgo object spans multiple states, and all_states is set on: from pymol import cmd set all_states,1 cmd.load_cgo([COLOR,1,1,0,SPHERE,3,0,0,1],name="bla",state=2) cmd.load_cgo([COLOR,1,0,0,SPHERE,0,0,0,2],name="bla",state=3) ray This happ

[PyMOL] Segmentation fault with PyMol V 1.3: pymol-v1.3-Linux-x86_64-TclTk8.5.tar.bz2

Hello: I always receiving a segmentation fault with pymol-v1.3-Linux-x86_64-TclTk8.5.tar.bz2. It also happens with pymol-v1.3-Linux-x86-TclTk8.5.tar.bz2 but not all the time. Here is how the segmentation fault happens. 1) read in a molecule ... a small one for testing purposes ... one that sho

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.  

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

Hi, I have a similar problem to Ben in this post: http://sourceforge.net/mailarchive/message.php?msg_id=20100512182803.GA21563%40crystal.harvard.edu I am using the svn r3910 with various versions of python and tcl/tk. I see the following message: IRQ's not enabled, falling back to busy waits: 2

Re: [PyMOL] segmentation fault -- fedora 13

Abbey Subject: [PyMOL] segmentation fault -- fedora 13 To:pymol-users@lists.sourceforge.net Message-ID:<4c1a5e43.7010...@biomaps.rutgers.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Help, I'm getting a seg fault on fedora 13. What could be w

[PyMOL] segmentation fault -- fedora 13

Help, I'm getting a seg fault on fedora 13. What could be wrong? Kevin ===== pymol Segmentation fault (core dumped) more /etc/fedora-release Fedora release 13 (Goddard) ldd pymol.exe linux-gate.so.1 => (0x5000) libpthread.so.0 => /lib/libp

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

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

Hi, One of my users is getting this: PyMOL(TM) Incentive Product - PyMOL Executable Build Copyright (C) 2009-2010 Schrodinger, LLC This PyMOL Executable Build is available only to PyMOL Power, Casual, and Developer Users who have a valid license to use this software product. Any other usa

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

[PyMOL] segmentation fault!

Dear All, I run pymol on laptop ubuntu 9.10 with ATI raedon gaphic card. when I try to call plugin of pymol for APBS, pymol crashes with segmentation fault message. Every suggestion would be welcomed! Thanks, Mehdi __ Do You Yahoo!? Sie si

Re: [PyMOL] Pymol segmentation fault

y, 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

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

Re: [PyMOL] Pymol segmentation fault

] 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 sel

[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

[PyMOL] Segmentation Fault / Bus Error

Hey Folks - I am trying to assign colors via APBS plugin to a surface which fails with a Bus error on Mac and Segfault on Linux. Versions are 1.1r2pre on Linux and Mac, as well as the latest from svn- trunk on Mac as well... The command that actually fails is ramp_new, as I found out by doin

[PyMOL] Segmentation Fault while running on NVIDIA 177.80

When I try to run pymol, it starts up fine but if I go to "Help > About PyMOL" or "Plugin > APBS Tools > Run APBS" then I get a message that says "Segmentation fault" and all the windows close. I have tried this on two machines. One has an Nvidia Quadro FX 3700. The other has a GeForce 7900. Both a

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

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

Hi, I found a critical and reproducible bug using the 0.99rc6-binarys on my machine. Stepps: - starting pymol from a kde terminal with user-rights - loading a pdb-file (e.g. 1K5D from pdb-database) - rotate the molecule with the mouse in any direction - hitting "Esc" to get to the commandline-mod

RE: [PyMOL] PyMol segmentation fault while starting from external python program

Update: With respect to "import pymol", I think all of the reported segmentation fault and race conditions have now been eliminated from the very latest source code. Since everyone doesn't have CVS access, I have posted a source tar-gz file on http://delsci.com/beta with updated instructions on b

RE: [PyMOL] PyMol segmentation fault while starting from external python program

din [mailto:brynd...@msu.edu] > Sent: Tuesday, October 11, 2005 5:06 AM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] PyMol segmentation fault while starting > from external python program > > Warren > > It seems like PyMol should have

RE: [PyMOL] PyMol segmentation fault while starting from external python program

ber 10, 2005 2:33 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] PyMol segmentation fault while starting from > external python program > > Launching PyMol form external python script will produce > segmaentation fault. > For example starting "launch.py" fr

[PyMOL] PyMol segmentation fault while starting from external python program

Launching PyMol form external python script will produce segmaentation fault. For example starting "launch.py" from "/pymol/examples/launching" -- $ python launch.py zsh: segmentation fault python launch.py -

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

[PyMOL] Segmentation fault when selection is too large

Hello, I use a script to build pml script file for PyMOL. Sometimes, the selection of individual residues are huge for PyMOL (0.98 or 0.97) and produces a segmentation fault. Is there a way to avoid this behavior ? Like a configuration file with a manageable memory quantity ? Thanks -- Sébast

Re: [PyMOL] Pymol segmentation fault - fedora core 1

On Mon, 26 Jul 2004 10:40:47 +0100, Roger Dodd wrote: Hi everyone, I've recently updated to the 0.97 release of pymol and although it ran fine to start with, it's now generating a segmentation fault. I installed from the * pymol-0_97-bin-linux-libc6-i386.tgz*

[PyMOL] Pymol segmentation fault - fedora core 1

Hi everyone, I've recently updated to the 0.97 release of pymol and although it ran fine to start with, it's now generating a segmentation fault. I installed from the * pymol-0_97-bin-linux-libc6-i386.tgz*

[PyMOL] Segmentation Fault

Dear PyMOL Users, This may have been answered before but I haven't found the answer yet. I have a script that has to iterate over a very large selection of atoms and when it runs it comes to a point where pymol shuts down and I recieve the message "Segmentation Fault" in my terminal window. I'