This page is only relevant for BUSTER releases between January 2011 and July 2011. For releases after this see update page BusterShortRefineTest2
The BUSTER short refinement test is distributed with BUSTER, in directory
samples/autobuster
You should run it as a normal user, in a directory you own, by
% mkdir buster-samples % cd buster-samples % . /path/to/buster/suite/setup.sh % cp $BDG_home/samples/autobuster/* . % ./refine_test.sh
Its main purpose is to check that you have correctly installed the BUSTER suite and the ccp4 tools that it uses. Check that the R/Rfree value returned is roughly 0.2237 / 0.2527:
% grep best refine_test.log
best refinement in BUSTER-GELLY-TNT reached for FP,SIGFP with R/Rfree 0.2237/0.2527
It also demonstrates the -M ShortRunVoid macro (see AutoBusterShortRunMacros page) for quickly performing some refinement and generating a map - this is the option you should be using after rebuilding small parts of a model in coot - and mentions the visualise-geometry-coot tool which can be used to look at the map and at the regions where BUSTER thinks the geometry is imperfect.
The script demonstrates how BUSTER can regularize a model after tweaking and how good a map BUSTER can generate in a couple of CPU-minutes.
The example is drawn from the final step (M) of the Student level introduction to autoBUSTER tutorial refining dopamine after it has been placed into a model of SULT1A3.
Note that BUSTER by default uses all the cores you have, though you can change this with the -nthreads option.
If the working directory and the CCP4 and BUSTER installations are all on a network drive, a gigabit network will improve the performance immensely - or install everything on a local hard drive.
| Eight-core Xeon E5420 | 2.50GHz | 94 seconds |
| Four-core Core 2 Q9650 | 3.0GHz | 157 seconds |
| Two-core Core 2 6700 | 2.66GHz | 213 seconds |
| Two-core Athlon 64 4400+ | 2.26GHz | 419 seconds |
Page by Tom Womack, Andrew Sharff and Oliver Smart original version 28 January 2011. Address problems, corrections and clarifications to buster-develop@globalphasing.com