[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 20:52:04 PST 2010


  Hi Mark,

tomorrow I will a post a link to some detailed description of underlying 
algorithms and examples.

Pavel.

On 12/14/10 7:34 PM, Mayer, Mark (NIH/NICHD) [E] wrote:
> 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
> differences.
>
> Mark
>
> ________________________________________
> 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:
>
> http://www.phenix-online.org/download/nightly_builds.cgi
>
> 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!
>
> Thanks,
> Pavel.
>
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