[Chimera-users] coloring carbon and deleting hydrogens

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 4 13:28:14 PDT 2006

Hi Narender,
There are several ways to accomplish each of those things.

(1) Coloring atoms differently from surface:
The command way is the shortest.  For example,
   color green,a C
will color carbon atoms but not their surfaces green, and
   color hot pink,s C
will color the surfaces of carbon atoms but not the atoms hot pink.

A longer way is to select the atoms you want to color and then use the 
Actions...Color menu. In that menu, first set the target to 
"atoms/bonds", then use the menu again to do the coloring.  If you 
choose the dotted line at the top of the menu, that "tears off" the 
menu so it stays open until closed.  After the coloring, you might want 
to set the target in the menu back to "all of the above" so it won't be 
confusing later.

Since the surface is in the way for selecting by clicking on the atoms, 
you might want to hide the surface, select the atoms, and then re-show 
the surface (or, use a command or the Select menu to select the atoms 
instead of picking from the screen). You can toggle the whole surface 
hidden/shown using the Model Panel.

(2) Undisplaying hydrogens:
if you want the hydrogens to be surfaced but not shown, they should be 
undisplayed rather than deleted.  The following command would undisplay 
all hydrogens:
   ~display H
Or, you could use Select...Chemistry...element...H and then 
Actions...atoms/bonds... hide.  If you delete the hydrogens, however, 
there would not be "holes" in the surface; instead, the surface would 
be recomputed for the structure without them.  So maybe you really do 
want to delete them, for example:
    delete H

You might want to take a look at the Getting Started tutorials 
(Help...Tutorials); one uses mostly the menu, one uses mostly commands, 
so you could pick the approach you prefer.
I hope this helps,

On Aug 4, 2006, at 11:57 AM, Narender Singh Maan wrote:

> Dear all,
> I am trying to show two residues of a protein structure with 50% 
> surface transparency along with a stick model (rest of the protein is 
> 0% surface transparent). Now in this i am having trouble in showing 
> those stick residues in a different color (for e.g. the default for C 
> atom is gray, which i want to show in green). Is there anyway in which 
> i can do it?. also for those two residues i want to delete the 
> hydrogens (only in stick, and not in surface representation)? any 
> suggestions would be of great help.
> Thank you
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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

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