[Chimera-users] surface transparency to particular residues

chemocev marker jirivitali at gmail.com
Sun Nov 20 02:17:41 PST 2016

Dear Elaine
Thanks for your help and its works very well now.


On Fri, Nov 18, 2016 at 8:09 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> surface
> trans 50,s :tyr
> trans 75,s :.a
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>
> …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.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
> I hope this helps,
> Elaine
> ---------------
> 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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