[Chimera-users] Surfaces and transparency

[Elaine Meng]

Hi Lothar,
It is not related to the VDW parameters, but to automatic classification of sets of atoms and excluding them from what is (by default) enclosed in a surface.  For example, people usually don't expect their ligands, solvent, or metal ions to be lumped together with the macromolecule, so there are automatically defined groupings:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats>

You can use "surfcat" to group the atoms any way you want, however.  E.g. commands

surfcat mystuff :adp,mg
surface mystuff

The ion is shown as "sphere" (full VDW radius) and if colored separately may show "through" the surface unless you make it smaller, and surface is "chunky" unless you increase vertex density.

repr bs :mg
surface mystuff vertexDensity 10

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

The transparency command works fine for the molecular surface EXCEPT when the surface  has custom coloring by vertex (electrostatic potential, for example).  For custom coloring by vertex you would have to specify the transparency at the time of coloring.

For example, either of these works fine for the surface that I showed with the commands above, as it was just shown in the initial tan color:

trans 50,s
trans 50,s #0

However, you can color by atomic patch and have it retain its transparency, e.g. the following command applies heteroatom coloring to the atoms in mystuff (ADP, MG although they were already colored that way) as well as the corresponding atomic patches in the molecular surface:

color byhet mystuff

Or something like this  will also color both the atoms and the corresponding patches in the molecular surface while the surface retains transparency:

color orange :adp

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 26, 2020, at 11:20 AM, Esser, Lothar (NIH/NCI) [E] <esserlo at mail.nih.gov> wrote:
> 
> 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