[Chimera-users] seeing atom info through surface

Fabian Glaser fglaser at techunix.technion.ac.il
Thu Aug 21 11:22:18 PDT 2008

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,


Quoting Elaine Meng <meng at cgl.ucsf.edu>:

> 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
> >>
> >>

More information about the Chimera-users mailing list