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: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...
(or you can see that by clicking the Help button on the Find Clashes/Contacts dialog) command version: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...
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 clashing. I hope this helps, Elaine ----- 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