[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?

Pavel writes:

> 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.

Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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