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 color. Best, Fabian 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@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@tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396