[phenixbb] phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups

Pavel Afonine pafonine at lbl.gov
Tue Dec 14 18:45:35 PST 2010

  PHENIX users:

starting dev-610 (development version of PHENIX) there is a new tool 
available for completely automated partitioning a model into TLS groups:


To run:

phenix.find_tls_groups model.pdb

or if you have a multiple CPU machine:

phenix.find_tls_groups model.pdb nproc=N

where N is the number of CPUs available (thanks Nat for 
parallelization!). There is no parameters that a user is supposed to 
tweak (except defining the number of CPUs, if desired).

The result of running the above command are atom selections that define 
TLS groups. These atom selections are ready to use in phenix.refine.

This is available from PHENIX GUI too, where automatically defined TLS 
groups can be readily visualized and checked on the graphics (thanks Nat!).

The algorithm is fast.
For example, for a GroEL structure (3668 residues, 26957 atoms, 7 
chains) it takes only 135 seconds using 1 CPU, and 44 seconds using 10 
CPUs. Analogous job takes 3630 seconds using TLSMD server.
For a lysozime structure it takes 9.5 seconds with one CPU, and 2.5 
seconds using 10 CPUs. The timing results may vary depending on the 
performance of your computer.

There is ongoing work that will slightly improve phenix.find_tls_groups 
within the next few weeks / a month; however the current version is 
functional and can be tried now. An example of such improvements are 
analyzing (scoring) user-defined TLS groups (for example, TLS groups 
from PDB file header), automated combining cross-chain TLS groups 
(non-contiguous segments) that will be obtained through connectivity 
analysis, better handling non-protein chains, and more. Integration with 
phenix.refine is also planned.

Any feedback is very much appreciated!


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