[Chimera-users] seeing atom info through surface

Fabian Glaser fglaser at technion.ac.il
Thu Aug 21 09:37:27 PDT 2008

Hi Elaine,

Almost.... The feature works, but the atoms are only "seen" in cpk 
representation, which make them appear over the surface itself. When I 
tried to reduce their radii with vdwdefine -0.2, the surfaces looses its 



Elaine Meng said the following on 20/08/08 21:10:
> 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,
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect> 
> After the surface is unselectable, the balloons should show 
> information on the underlying atoms.  I hope this helps,
> Elaine
> -----
> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 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

Fabian Glaser, PhD

Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL

Web:   http://bku.technion.ac.il
Email: fglaser at tx.technion.ac.il
Tel:   +972-(0)4-8293701
Cel:   +972-(0)54-4772396

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