[Chimera-users] positive and negative overlaps

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 3 08:51:36 PST 2010

Hi Kshatresh,
Basically "overlap" is the overlap of the VDW surfaces of the atoms.   
Think of the atoms as spheres with their VDW radii: where the spheres  
interpenetrate each other, there is positive overlap.  Where the  
spheres exactly touch, there is zero overlap.  Where the spheres are  
not in contact, the distance between their surfaces is the magnitude  
of negative overlap (if the sphere surfaces are 1 angstrom apart, the  
overlap is -1).  There is also an optional adjustment of the overlap  
value for potentially H-bonded atoms, because studies have found that  
H-bonded atoms' effective radii are smaller.

The documentation includes full descriptions of the meaning of  
overlap, contacts, and clashes, as well as recommended cutoff values:

   (or you can see that by clicking the Help button on the Find  
Clashes/Contacts dialog)

command version:

If you prefer to think of atoms as points, you can concentrate on the  
distances column of the results rather than the overlaps.  However,   
the overlaps are a little more physical, because they take into  
account the different VDW radii of different types of atoms.  If you  
just use a single distance cutoff for all atom types, the smaller  
atoms might not really be in contact whereas large atoms might even be  

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 3, 2010, at 5:43 AM, Kshatresh Dutta Dubey wrote:

> Dear all,
> Can anyone tell me the significance of positive and negative  
> overlaps  results in structure analysis module of chimera, as i got  
> 140 contacts that contains both positive and negative overlap values?
> Any help is appreciated.
> Thanks in advance
> Kshatresh Dutta Dubey

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