[phenixbb] automating setting up parallel refinement jobs

Donnie Berkholz dberkholz at gentoo.org
Thu Feb 17 16:21:22 PST 2011

On 15:42 Thu 17 Feb     , Nathaniel Echols wrote:
> On Thu, Feb 17, 2011 at 12:02 PM, Kendall Nettles <knettles at scripps.edu> 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.
> >
> >  I think this would really speed things up for your industrial users. I'm working on 20 structures of the same protein with different ligands, and expect to spend maybe 8 hours generating TLS groups and editing the 240 parameter files. A GUI interface would make it 10 or 20 minutes!
> I did something like this for Phaser as a proof-of-concept for simple
> parallelization of tasks:
> http://cci.lbl.gov/~nat/img/phenix/phaser_mp_config.png
> http://cci.lbl.gov/~nat/img/phenix/phaser_mp_results.png
> It runs all search models in parallel, and can sample multiple
> expected RMSDs too.  The calculations can be parallelized over
> multiple cores (I never tried more than 12, I think, but there's no
> limit that I'm aware of) or across a cluster.  It only uses one
> dataset with many models, but I could have just as easily done the
> reverse, or both model and data parallel.  This isn't a very
> sophisticated program (it was maybe 2 days effort), but eventually
> we'll have a new MR frontend that does something similar, with lots
> more pre-processing of search models.

Intriguing. I'd really love to see it also run over resolution limits in 
parallel, so you could do a test like Figure 1(a) in this recent Acta 

Bjørn P. Pedersen, J. Preben Morth and Poul Nissen. "Structure 
determination using poorly diffracting membrane-protein crystals: the 
H+-ATPase and Na+,K+-ATPase case history" Acta Cryst D66: 309-313 


Donald S. Berkholz, Ph.D.
Research Fellow
James R. Thompson lab, Physiology & Biomedical Engineering
Grazia Isaya lab, Pediatric & Adolescent Medicine
Medical Sciences 2-66
Mayo Clinic College of Medicine
200 First Street SW
Rochester, MN 55905
office: 507-538-6924
cell: 612-991-1321
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