This may be a silly question (usually doesn't stop me), but does running pymol single-threaded (or on a single-core system) make any difference?
I was a bit surprised to see pthread in the stack trace you linked to. Pete Witek Kwiatkowski wrote: > Hi, > > I think that this is related to general pymol problem in ubuntu 8.10. > We had exchanged couple emails with Warren about this but I have not > heart back from him since. > It seems that there is a bug in pymol or Tkinter library and whenever > pymol tries to open special kind > of window it crashes with segfault. (try to open Help -> About Pymol) > (that bug is present in both python 2.4 an 2.5 > and none of pymol versions works.) > see also > https://lists.ubuntu.com/archives/universe-bugs/2008-November/019193.html > > Witek > > Pete Meyer wrote: >> Two suggestions... >> Check that the coordinate fields in your pqr file are separated by >> spaces (some pdb to pqr converters don't always do this in my hands, >> probably due to large negative coordinate values). Also, try using your >> .pqr file and .in file to run apbs from the command line and see if it >> segfaults there. >> >> Pete >> >> Talavera wrote: >> >>> Hi there, >>> >>> Whenever I tried in Pymol to load the .pqr file to represent the >>> electrostatic surface the program crashes with Segmentation fault. I am >>> using a laptop with Ubuntu 8.10. Does any of you have any suggestion for >>> this problem. >>> >>> Thanks a lot in advanced. >>> Ariel >>> >>> ************************************************* >>> Ariel Talavera Perez, PhD >>> Center of Molecular immunology >>> calle 216 esq. A 15, Atabey, Playa >>> Havana 11600, CUBA >>> email: [email protected] >>> ************************************************* >>> >> >> >
