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

Feldman-Salit, Anna anna.feldman-salit at h-its.org
Sat Apr 24 13:16:09 PDT 2010

Dear Elaine,

I appreciate a lot your detailed and quick response!

My best wishes,

From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Saturday, April 24, 2010 7:37 PM
To: Feldman-Salit, Anna
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] "cutoff" parameter in Find clashes/contacts option

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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