[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
>
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>
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>
>
>
>
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