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