[Chimera-users] Re: [chimera-dev] Strange behavior, crashing, etc.

chimera-users at cgl.ucsf.edu chimera-users at cgl.ucsf.edu
Thu Apr 24 15:30:25 PDT 2003

Hi Geoff,

  Eric Pettersen tells me Chimera is hanging when you display
diamond.pdb in ball and stick or sphere mode because it is searching
for rings.  There are too many rings to find.  Eric will look at
fixing the ring finding code.  The reason it needs to know the rings
for some display modes is so it can identify atom types (classed by
connectivity) so it can assign correct atom radii.  You can work
around the problem by issuing a Chimera command to set the vdw radii
before using ball and stick or sphere display.  Use Favorites/Command Line
and type a command like

       vdwdefine * * 1.0

This example sets all atom radii to 1 angstrom (for sphere display).
See the User's Guide under Commands for details on setting the radii
of specific atoms if you want different atoms shown with different sizes.

  Any application, Aqua or not, can have an icon in the Dock -- it just
has to be packaged with the Mac App directory layout and have an icon file.
But Force Quit apparently only lists Aqua applications.  The Aqua version
of Chimera is shown in the Force Quit list.


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