[Chimera-users] smoothening the edge of molecular surface

[Elaine Meng]

Hi Maurice,
There is not complete control of the edges when you show part of a  
molecular surface, but there are ways to try to improve the appearance:

Which triangles are shown:
(A) Hiding or showing the surface with the Actions menu and/or the  
"surface" command only sets the surface per atom; you either get all  
the surface that comes from that atom or none of it.  However, you  
can carefully choose which atoms' surface patches are shown  
(admittedly this can be difficult).

(B) The Surface Zone tool (under Tools... Surface/Binding Analysis)  
allows independent control of triangles even if they come from the  
same atom.  It turns triangle display on/off based on distance from a  
selected set of atoms.  The advantage is that the edge will not be as  
rough as if you were restricted to per-atom patches.  Disadvantages  
are that you need to have some atoms that are suitable for defining  
the zone, and the zone is spherical for each selected atom.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfzone/ 
surfzone.html

Clipping:
Even if you have the best set of triangles possible, the edge will  
still show the triangle shapes.   However, the surface can be sliced  
cleanly with a clipping plane.  The limitation is that planes are  
planar!
(A) global clipping planes as shown in the Side View - these clip  
everything, and are always normal to the line of sight
(B) per-model clipping (under Tools... Depiction) - can clip the  
surface only, and can face in any direction
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/ 
per-model.html

Change the triangles by changing surface parameters:
If you select the surface with Ctrl-click and open the Selection  
Inspector, you can then change various parameters of "MSMS surface":
(A) turning off "show disjoint surfaces" will omit additional surface  
bubbles within the structure that may be making the view more  
complicated.
(B) increasing "vertex density" will make the triangles smaller
etc.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html#msmsprop

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Jun 6, 2008, at 1:20 AM, Maurice Ho wrote:

> Is there any way to smoothen the edge of molecular surface when  
> only part of it would be displayed? It's quite often that a couple  
> of triangles sticking out from the edges which makes the image a  
> bit absurd.  Please kindly advice.
> rgds,
> Maurice Ho