[Biojava-l] JMol I/O

[Andreas Prlic]

Hi Andy,

probably you are trying to visualize a small molecule in Jmol, but the
visualization script you are sending  only works if you have several
C-alpha atoms available. Try something like "select * ; spacefill
on;". Jmol has a powerful scripting language which is probably worth
having a look at, if you want to work with it more closely.

Andreas

On Sun, Nov 15, 2009 at 2:07 PM, Andy Lu <andylu0320 at gmail.com> wrote:
> Hi, sorry to bother everyone again.
> But I have a simple quesiton, I am using the SimpleJMolExample.java provided
> on the website and it works. But for a pdb file containing about 20 atoms,
> all of the atoms shows up on JMol for 1 second and then disappears, is it
> because the color changes or something or some atom size restriction? It
> works for files that contain much larger number of atoms.
> If I try to open a file manually from JMol through the open option, it shows
> up nicely. Is there a way that I can make the pdb file displayed on JMol
> through Biojava the same color/display as the one if I open it manually
> though JMol?
> Any help would be greatly appreciated!
> Thank you!
>
> --
> Andy Lu
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