[Chimera-users] seeing atom info through surface

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 21 10:53:30 PDT 2008

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.

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

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