[Chimera-users] "cutoff" parameter in Find clashes/contacts option

Elaine Meng meng at cgl.ucsf.edu
Sat Apr 24 10:37:33 PDT 2010

Dear Anna,
The cutoff is the amount of VDW overlap for a pair of atoms to be  
listed in the results. The VDW overlap is the distance between their  
VDW surfaces: if you think of the atoms as balls with the VDW radii,  
if they intersect the overlap is positive, if they exactly touch the  
overlap is zero, and if they are farther apart the overlap is negative.

So if you use a zero cutoff you will get only pairs that touch or  
intersect.  If you use a -0.4 cutoff you will get only pairs whose VDW  
surfaces are within 0.4 angstroms of each other (which could include  
pairs that are close but not touching, or touching, or intersecting).   
The more negative the cutoff, the more results you will get.

The results from findclash include both the VDW overlap distances  
("overlap") and the distances between the atom centers ("distance").

The definition of overlap is in the findclash page, but I agree it can  
be confusing.  It was also discussed in a previous post.

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 Apr 24, 2010, at 3:22 AM, Anna Feldman-Salit wrote:

> Dear All,
> I was unsuccessfully looking for the explanation to what exactly  
> "cutoff" parameter means.
> I'm using the Find clashes/contacts option to identify the contacts  
> and not clashes, by assigning the default values of -0.4A and 0.0   
> to "cutoff" and "allowance" parameters. However, I do not understand  
> how it is used.
> I would very much grateful for the information, since I also want to  
> include it in my dissertation.
> Best regards,
> Anna Feldman-Salit

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