[phenixbb] How do different sections of TLS groups affect refinment

Pavel Afonine PAfonine at lbl.gov
Wed Jan 20 14:25:44 PST 2010

Hi Aaron,

TLSMD server suggests you possible optimal selections for TLS groups. If 
I remember correctly, it gives you a list of 20 options or so.

It's up to you which one to choose. Usually you look at the graphic 
"residual vs number_of_tls_groups" and see at which point the curve 
stops dropping sharply. Also, you need to use common sense too, say, I 
wouldn't choose a set of TLS groups that brakes a helix into multiple 
parts. I'm actually puzzled about how that happened. I think it is a 
good question for Ethan Merritt, the author of TLSMD tool.

Also, you may want to try a few possible TLS separations and see which 
one gives your better refinement results.


On 1/20/10 1:38 PM, Bart, Aaron G wrote:
> Greetings everyone,
> I am still fairly new to crystallography, so forgive me for my
> naivety.
> My question involves how the TLSMD server segments my protein
> and the effects it has on refinement. For instance when i use
> "Multi-Chain Alignment Analysis", which lines the sequence for
> all of my chains (a total of 12) and shows how TLS groups are 
> divided among them, it shows varying selections of TLS groups
> among the different chains. It should be noted that the sequence
> is the same for all the chains in my protein.
> Also if a TLS group splits a alpha helix into multiple parts, would 
> this be valid? I have come to understand that helices move more like
> rigid bodies than segmented groups...
> Thanks!
> -Aaron
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