Hi Tania, Normally one would use the option (your #2) to ignore pairs of atoms that are directly bonded or only a few bonds apart, because they are often closer than you would expect from their VDW radii. In other words, they would often be identified as clashes, as you described. For this reason, we recommend using the default setting to ignore pairs of atoms that are 4 or fewer bonds apart (or at least 3) when identifying clashes. They are not really clashes, the atoms are close together because of covalent bonding. We allow users to adjust N to give more freedom, but 4 is recommended. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...

I should also mention that using Rotamers (or swapaa) will not always give zero clashes. Depending on the structure, all of the rotamers may have some clashes, so even if you use clashes to choose the rotamer, it will be the one with the fewest clashes, not necessarily zero. However, the "clashes" you listed will probably mostly go away if you use the option to ignore atoms within a few covalent bonds of each other (your #2). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h...

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 6, 2010, at 7:42 AM, Kirys, Tatsiana wrote:

Dear All, i'm trying to figure out scheme for calculating protein amino acid clashes. I've read in User's Guide that

1) The overlap between two atoms is defined as the sum of their VDW radii minus the distance between them and minus an allowance for potentially hydrogen-bonded pairs:

overlapij = rVDWi + rVDWj – dij – allowanceij

2) It has an option: Ignore contacts of pairs [ N ] or fewer bonds apart (N=4 by default).

i calculated rotamer clashes from "Penultimate rotamer library" according to 1) and there are clashes between

N ans C N and CB N and CG CA and CG CA and OD1 etc.

i'm sure i do something wrong because "Penultimate rotamer library" was checked for the clashes.

I dont understand why 2) option exists, what is the physical meaning of it? and why N can be cosed arbitrary? many thanks Tania