[Chimera-users] surface transparency to particular residues

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 18 11:09:08 PST 2016

Hi Jiri,
Welcome to Chimera!

Sure, if it is a molecular surface, you can specify acting only on the surface patches from specific atoms, and this applies to not only transparency but also coloring and display status (hidden or shown).

If you select some atoms (by any method, with mouse, Select menu, “select” command, using Sequence window, etc.) then the menu: Actions… Surface… transparency… will affect only the surface patches from those selected atoms.  If you want to use the mouse to select some atoms but the surface is in the way, you can temporarily hide the whole surface using the “S”hown checkboxes in the Model Panel (under Favorites in the menu).

Or if you are using the “transparency” command there is no need to select, you can specify the atoms directly, e.g.

open 1zik
display protein
trans 50,s :tyr
trans 75,s :.a


…those examples acting on the surface patches (the “,s” means surface only) of tyrosine and chain A atoms.  Now, whether it is a good idea to make patches within a surface transparent is a separate matter.  It can give a confusing image if you are not careful.

You may be interested in the “getting started” tutorials for menu/GUI and command control of Chimera.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 18, 2016, at 10:47 AM, chemocev marker <jirivitali at gmail.com> wrote:

> HI All
> I am completely new to chimera and I am wondering if there is a way to set the surface transparency to just a particular region, not to the whole surface. 
> best
> Jiri

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