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 <[email protected]> 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 > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
