Re: [phenixbb] automating setting up parallel refinement jobs

On 15:42 Thu 17 Feb , Nathaniel Echols wrote:

On Thu, Feb 17, 2011 at 12:02 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.

 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 paper: 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 (2010). -- Thanks, Donnie 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