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

Hi Fabian, To have the balloons show the atom info, the atoms must be displayed, but they do not have to be visible; they could be behind opaque surface. You don't need to make the atoms stick out by showing them as cpk. However, if you want to see the atoms (not just their info) at the same time as the surface, just make the surface slightly transparent (for example, Actions... Surface... transparency... 30%). Later you can change it back to 0% if you want. I would probably show the atoms as wire or stick, not cpk. Changing the VDW radii does not make the atoms only shrink, it also regenerates the molecular surface based on the new radii. In my tests, that did not change the surface color, but maybe it depends how the surface was colored in the first place. If you can list the steps that give this behavior, you could use Help... Report a Bug in the Chimera menu to send us that information. Ignoring that issue, there is still no reason in this case to change the VDW radii - it is unrelated to showing the atom information balloons. Best, Elaine On Aug 21, 2008, at 9:37 AM, Fabian Glaser wrote:

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

Hi Fabian, Both the atom spheres (CPK representation) and molecular surface are triangulations rather than the exact smooth surfaces, and when both are shown, parts of the spheres poke through above the surface. The ideal surfaces would overlap exactly, at least in the convex areas, so even then you might expect some show-through, although it wouldn't look so bumpy. The simplest way to avoid it is to use a different atom representation. However, you must be doing this for some reason, so here is my best idea: You could "fake" the CPK representation by using ball-and-stick instead, but with increased ball scale factor (ballScale=0.25 by default, whereas 1 would give the VDW radius and be the same as the CPK representation). The ball scale factor can be changed in the Selection Inspector ("molecule model" section), or in the molecule model attributes panel, or with a command something like: setattr m ballScale 0.85 <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> 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 21, 2008, at 11:22 AM, Fabian Glaser wrote:

Thanks for your answer. But even if teh surface is 0% transparent I see the CPK balls "sticking out", and they don't look nice. Maybe there is a way of slightly enlarging the surface?

THanks a lot for your kind help,

Fabian