[phenixbb] automating setting up parallel refinement jobs

Kendall Nettles knettles at scripps.edu
Thu Feb 17 12:02:42 PST 2011

Dear PHENIX developers, 

I'm writing to ask if it would be possible to automate the following: 

What we do now is a series of parallel throw away refinements to test for different parameters. So I will set up 12 folders with the same data and different parameter files (and all the same file names). On top of individual sites and adp I would add:

1=nothing (control)
3=fix_rotamers = True
4=flip_peptides = True
5=nqh_flips = True
7=tls with 3 groups per monomer
8=tls  with 6 groups per monomer
9=tls  with 9 groups per monomer
10=tls 1 with 12 groups per monomer
11=tls 1 with 15 groups per monomer
12=tls 2 with 20 groups per monomer

I then launch all of them with a script that sends it to a cluster. After reviewing results, we combine parameters for one job that we keep. 

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 don't see a way to select different TLS groups. I really prefer to test different ones myself for comparison, at least to convince myself that the auto selection is superior. We see big differences from optimizing TLS group number. Right now I am asking TLSMD to generate all these tls files, copying them to my desktop, copying to parameter files. Help!

All the best, 

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