[phenixbb] Multiple TLS groups per molecule

Nathaniel Echols nechols at lbl.gov
Sun Nov 13 17:18:54 PST 2011

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:



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