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. -Yarrow -Yarrow

On Sun, Nov 13, 2011 at 5:10 PM, Yarrow Madrona 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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