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
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. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004882.html> 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 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
Dear Elaine, I appreciate a lot your detailed and quick response! My best wishes, Anna ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Saturday, April 24, 2010 7:37 PM To: Feldman-Salit, Anna Cc: chimera-users@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. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-March/004882.html> 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 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
participants (3)
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Anna Feldman-Salit -
Elaine Meng -
Feldman-Salit, Anna