[Chimera-users] seeing atom info through surface

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 20 11:10:38 PDT 2008

Hi Fabian,
Just a few days ago we discussed this issue and added the following  
to the documentation:

By default, placing the mouse cursor over an object such as an atom,  
bond, or surface (without clicking any buttons) will show its label  
information in an atomspec balloon. The atomspec balloon indicates  
what would be selected by picking at the current position, but more  
generally, it is useful for identifying objects without displaying  
their labels. Sometimes one would rather see information for the  
atoms under a surface than for the surface itself. This can be  
achieved by making the surface unselectable with the mouse, for  
example by:

    1. selecting the surface, either picking it with the mouse or  
using the Model Panel
    2. opening the Selection Inspector, by choosing Actions...  
Inspect or clicking the button near the lower right corner of the  
main Chimera window
    3. in that dialog, inspecting Surface and changing selectable  
with mouse to false

...the above appears in the "Selection" man page,

After the surface is unselectable, the balloons should show  
information on the underlying atoms.  I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 20, 2008, at 11:01 AM, Fabian Glaser wrote:

> Hi Tom,
> First, thanks a lot to you, to Sunhwan, Elaine and to you for  
> helping so much. Indeed the addition you mentioned solved the  
> problem, although additionally I installed delphi which works very  
> smoothly with chimera, but it's good in any case to have a way to  
> work with charmm output and to have both methods available.
> Secondly, I have a question regarding the surface potential itself:  
> Once the delphi run ends and I get the surface colour coded by  
> electrostatics, (or conservation, etc.) it would be very useful to  
> be able to know which residues is found in any specific negative or  
> positive potential region (or conserved). But when the surface is  
> shown, the cursor doesn't show the residue information as when the  
> cpk representation is on (like #0 THR 684.A), and therefore is not  
> easy to quickly find information about the residues of interest.
> Is there any way to overcome this limitation? It will be really  
> useful.
> Best regards and have a great day,
> Fabian

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