[Chimera-users] amino acid clashes

[Kirys, Tatsiana]

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