[phenixbb] automating setting up parallel refinement jobs
Francis E Reyes
Francis.Reyes at Colorado.EDU
Thu Feb 17 13:15:10 PST 2011
On Feb 17, 2011, at 1:02 PM, Kendall Nettles wrote:
> So here is my feature request: I would love to have a GUI interface
> to generate the folders and parameter files, where you would select
> a list of common parameters, and a list of parameters to populate 1/
> job, instead of having to set up each one as a separate job.
A talented bash scripter can get this done for you .
If you want a GUI, an even more talented Automator (OS X) scripter can
get this done for you. However, since you have 12 specific parameters
to run you shouldn't need a gui since the only input is the pdb and
data (run_refine_workflow.sh file.pdb file.mtz). Pulling out the r/
r_free out of each is a straightforward grep.
I've found that OS X Xgrid works for parallelization (I've got a
pipeline that paramaterizes Phaser searches, and it can run anomalous
FFT's, or rigid body refines of the solutions).
> Right now I am asking TLSMD to generate all these tls files, copying
> them to my desktop, copying to parameter files. Help!
Is phenix.find_tls_groups (in dev-610) not sufficient?
> PHENIX users:
> starting dev-610 (development version of PHENIX) there is a new tool
> available for completely automated partitioning a model into TLS
> 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
> 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!
Francis E. Reyes M.Sc.
University of Colorado at Boulder
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