Viewer - van der Waal's radii changes

We use Marvin viewer within our tool. We often find that in the spacefill or the ball and stick view mode, the van der waal's radii is different for different molecules. Is there a way to keep them the same - ie set it globally?





Also, the depth changes - how can we stop this and have uniform depth? Here what happens is that some molecules seem to hitting at you right at your eye while some are deep inside the cell.

Dear Sumathy,





How do you use Marvin viewer? (applet, beans, application)


If you have View menu, View>Rescale Cells>Uniformly sets the


van der waal's radii and the depth uniformly (using the smallest scale of the cells).





Erika

Dear Erika,





Thanks for your reply.





We use the APIs.





We tried the option you have suggested. It works but we are not comfortable with that smallest size of the cell. Can we set that to some other desirable size ourselves?





Thanks,





Sumathy

Use setAutoTabScale(boolean) and setTabScale(double) methods to set the scale value.


The scale is the displayed length of a C-C bond in pixels.


For example:

Code:

viewPane = new MViewPane(); double scale = 24.0; viewPane.setAutoTabScale(true); viewPane.setTabScale(scale);

Erika.