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 <tno...@gmail.com> 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 crash.
>
> So the segfault always happens when I do this:
>
> ~/bin/MacPyMOL.app/Contents/MacOS/MacPyMOL -p < incmd
>
> where the incmd file contains solely the test below:
>
> cmd.read_pdbstr("""ATOM 1 N MET A 1 -14.152 0.961 4.712
> 1.00 1.26 N\nATOM 2 CA MET A 1 -13.296 0.028
> 3.924 1.00 0.43 C\nATOM 3 C MET A 1 -11.822
> 0.338 4.193 1.00 0.41 C\nATOM 4 O MET A 1
> -11.358 1.432 3.941 1.00 0.68 O\nATOM 5 CB MET A 1
> -13.571 0.173 2.426 1.00 1.24 C\nATOM 6 CG MET A
> 1 -15.046 -0.135 2.144 1.00 1.63 C\nATOM 7 SD
> MET A 1 -16.174 1.270 1.982 1.00 2.41 S\nATOM 8
> CE MET A 1 -17.702 0.313 1.823 1.00 2.91 C\nATOM
> 9 N THR A 2 -11.121 -0.642 4.703 1.00 0.23 N\nATOM
> 10 CA THR A 2 -9.669 -0.447 4.998 1.00 0.19
> C\nATOM 11 C THR A 2 -8.861 -1.586 4.373 1.00 0.15
> C\nATOM 12 O THR A 2 -9.036 -2.736 4.724 1.00 0.20
> O\nATOM 13 CB THR A 2 -9.462 -0.447 6.516 1.00
> 0.20 C\nATOM 14 OG1 THR A 2 -10.399 0.505 7.010
> 1.00 0.31 O\nATOM 15 CG2 THR A 2 -8.090 0.103
> 6.896 1.00 0.23 C\n""","a")
>
> (its just a single line)
>
> I use PyMOL 1.5.0.1 on MacOS. Interestingly, it doesn't crash when the input
> line comprises about 5 to 7 atoms. Moreover, Pymol version 1.2r1 also
> crashes, but work until appx 20 atoms in a line.
>
> Best,
> Tim
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
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