[phenixbb] Multiple TLS groups per molecule

Yarrow Madrona amadrona at uci.edu
Tue Nov 15 07:27:43 PST 2011

As usual, very helpful.  Thanks!

One more question.  When you refine in subsequent rounds I read that
phenix.refine will refine as anisotropic because of the ANISOU labels
attached to the PDB. Is it necessary to enter something like
"stragegy=tls+isotropic"? I am just worried that if I explicitly ask for
individual isotropic refinement this might occur without tls refinement.



> On Sun, Nov 13, 2011 at 5:10 PM, Yarrow Madrona <amadrona at uci.edu> wrote:
>> I would like run TLS and individual isotropic refinement. I want to
>> separate one molecule into four TLS groups.  I havn't found
>> documentation
>> for this.
> You need to make selections like this:
> refinement.refine.adp {
>   tls = chain 'A' and resseq 1:25
>   tls = chain 'A' and resseq 26:50
>   tls = chain 'A' and resseq 51:75
>   tls = chain 'A' and resseq 76:100
> }
>> Is the number of TLS groups automatically done by phenix refine
>> when you tell it to run TLS refinement on the whole molecule?
> Right now the default behavior (which admittedly isn't ideal) if you
> don't give it explicit atom selections is to treat the entire molecule
> as a single TLS group.  We've discussed changing this to treat each
> chain (minus waters and ions) as a separate TLS group, but no one has
> had time to test the effects.  You can however use
> phenix.find_tls_groups within phenix.refine - either interactively
> through the GUI, or on the command line by adding this parameter:
> tls.find_automatically=True
> -Nat
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Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

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