[Chimera-users] Surfaces and transparency

[Esser, Lothar (NIH/NCI) [E]]

Hi,
  In making surfaces around ligands and making them transparent, I ran into some problems:

Using open/fetch 3NHA I have a molecule in front of me with ADP Mg bound.
Creating a surface around ADP is easy but it won't cover Mg at all. It seems that single ions like Mg and also single water molecules don't get surfaces around them. Is this because of default vdW values that need to be manually adjusted ?

Let's say I have a surface around ADP and want to make it transparent, I thought

Transparency 50,s #0

Should work but it did not. There are some work arounds using transparent colors through the use of colordef.
However, I had planned to color the surface by atom and used
   scolor #0 zone #0
which worked but I could not get it transparent with transparency statements. However, I can make atoms transparent then use

scolor #0 zone #0   #which makes the surface also transparent and hides the ball-and-stick model.
To make it show up I can use transparency 0,a #0 and again the stick model appears under the transparent surface.

Is there a simpler way ? A way that can be applied to other surfaces that were for instance colored with say potential, hydrophobicity, bfactor key etc ?

Thanks
Lothar





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