[phenixbb] rotamers

Donnie Berkholz dberkholz at gentoo.org
Fri Mar 25 08:53:13 PDT 2011

On 12:29 Thu 24 Mar     , Dale Tronrud wrote:
> Of the possible ways to represent this common situation I think 
> placing a side chain with occupancy set to zero is the worst.  For the 
> naive user (and that is not necessarly pejorative) it will lead them 
> to view the placement of those atoms as unwarrantably confident.  For 
> those with a deep understanding of the meaning of the parameters it is 
> flat wrong - it says that I know that this atom is never in this 
> location.
> If you want to be precise for the knowledgeable user you need to put 
> in a non-zero occupancy but assign it a very large sigma on your 
> SIGATM record for that atom.  Of course when naive users see SIGATM 
> records I expect their heads will explode.

Has anyone thought about putting them into a second MODEL record 
instead? That way, they're present for people who want them, but aren't 
shown by default in programs like PyMol. No clue how refinement programs 
would deal with this.


Donald S. Berkholz, Ph.D.
Research Fellow
James R. Thompson lab, Physiology & Biomedical Engineering
Grazia Isaya lab, Pediatric & Adolescent Medicine
Medical Sciences 2-66
Mayo Clinic College of Medicine
200 First Street SW
Rochester, MN 55905
office: 507-538-6924
cell: 612-991-1321
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