[phenixbb] automating setting up parallel refinement jobs

Kendall Nettles knettles at scripps.edu
Thu Feb 17 13:56:36 PST 2011


Hi Francis, 
We always scan different TLS groups. It makes at least 1% difference in the R/Rfree in every structure I've done. I haven't compared with the phenix version yet to see if we can drop this. 

Kendall 




On Feb 17, 2011, at 4:15 PM, Francis E Reyes wrote:

> 
> 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
> 
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
> 
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
> 
> 
> 
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb




More information about the phenixbb mailing list