Marvin3.0 upgrade

I have been using Marvin3.0 for a while now. I was upgrading my marvinbeans.jar file to the latest version but noticed some difference in the structure rendering.





First, the structures seem to be rendered in "Stick" rather than "WireFrame".





Second, in Marvin4.0 the bond thickness (in wireframe mode) are rescaled too much according the size of the structure. I like the rescaling in 3.0 but the one in 4.0 seems to make the bond in large molecules too thin and bonds in small molecules too thick. Is there a scaling factor I can control.





Any suggestion how to work this out?

Quote:

First, the structures seem to be rendered in "Stick" rather than "WireFrame".

If you are not sure in which rendering mode you are, check the settings in the "View->Display" menu.





If you have got any problem with line thickness, you can set it from the "Preferences" menu: "Appearence/Wireframe/Bond thickness".


You can also set it by the wireThickness parameter. You can specify it as an applet parameter or you can use it from API: MarvinPane.setParams("wireThickness=0.09\n").


If you want to specify the scaling factor, you can use the scale parameter.

I tried both wireframe thickness and scale factor. They don't seem to do what I really wanted. Basically the problem I am seeing here is that in marvinbean4.0, the bond thickness was automatically adjusted based on the size of the molecule. When the molecule is big (i mean mw around 500, the bonds are displayed as very thin lines and it is hard to see the whole molecule. In Marvin3.0, there seem to be a minimal bond thickness. No matter how big the molecule is the bond thickness remain the same. This gives a much consistent look across the grid when the size of the molecules in the same grid vary quite a bit. Is there a way to set the bond thickness to be uniform across the grid? I still want the molecule size to scale according to the table size though (basically setAutoTabScale(true)). Just don't want the bond thickness to change.





Thanks.

Quote:

Is there a way to set the bond thickness to be uniform across the grid? I still want the molecule size to scale according to the table size though (basically setAutoTabScale(true)). Just don't want the bond thickness to change.

In the current Marvin, you can not do this.


But we plan to create a drawing option where bond thickness will be always 1 pixel (not depending on the scalling factor).


I do not know yet when it will be ready but we will notify you when it is already implemented.