[Chimera-users] positive and negative overlaps

Kshatresh Dutta Dubey kshatresh at gmail.com
Wed Mar 3 17:39:39 PST 2010

Dear Elaine,

Thanks for your help, it clears my problem.



On Wed, Mar 3, 2010 at 10:21 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.html
> >
>  (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.html
> >
> 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
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