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