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

Mayer, Mark (NIH/NICHD) [E] mayerm at mail.nih.gov
Tue Dec 14 19:34:36 PST 2010

Great; look forwards to using,
A question for those of us who have been using TLSMD for a few years
is how the groups differ. You give timing comparisons for GroEL but
do not report if the TLS groups differ, and if they do, how much the
groups differ: e.g. is it a residue or two at the group ends, or larger


From: Pavel Afonine [pafonine at lbl.gov]
Sent: Tuesday, December 14, 2010 9:45 PM
To: PHENIX user mailing list
Subject: [phenixbb] phenix.find_tls_groups: a new tool for automated partitioning a model into TLS groups

  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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