[Chimera-users] amino acid clashes

[Elaine Meng]

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.html 
 >

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.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 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