BUSTER Short Refine Test from Nov 2012

Contents



Initial test of refine

$BDG_home/samples/autobuster
refine -h
 ##############################################################################
 # This software is licenced to : Global Phasing Ltd (hypatia) 
 ##############################################################################
 ##############################################################################
 ##   [refine] Framework for automatic refinement of macromolecules
 ##############################################################################
refine help output edited out

mkdir test
cd test
$BDG_home/samples/autobuster/refine_test.sh

Will run a refine job with -M ShortRunVoid this should take between 90 seconds and 400 seconds depending on machine speed
refine output will follow and also be written to  refine_test.log 

 ##############################################################################
 # This software is licenced to : Global Phasing Ltd (hypatia) 
more output edited out -see link below
 refine  task has finished. Will now grep the final R/Rfree 

 best refinement in BUSTER-GELLY-TNT reached for FP,SIGFP with R/Rfree 0.2001/0.2414

Please confirm that the R/Rfree value above is roughly 0.2001/0.2414
more output edited out -see link below
refine_test_screen_output.txt the full output that you will see on the screen
refine_test.log the actual refine log file
refine_test_dir.tgz compressed tar ball with the contents of refine_test.dir. This can be unpacked using tar xf refine_test_dir.tgz

Follow on test of visualise-geometry-coot

visualise-geometry-coot refine_test.dir

Follow on test of buster-report

buster-report -d refine_test.dir
 ##############################################################################
 ##   [buster-report] produce user-friendly report of a BUSTER run
 ##############################################################################
more output edited out -see link below
Have opened refine_test.dir-report/index.html for main report. Use firefox to view this:
  firefox refine_test.dir-report/index.html
buster-report_screen_output.txt the full output that you will see on the screen
refine_test_dir_report.tgz (file not found) compressed tar ball with the contents of refine_test.dir-report. This can be unpacked using tar xf refine_test_dir_report.tgz

Benchmark cpu figures

Normal termination (XXX sec)
mkdir test
cd test
$BDG_home/samples/autobuster/refine_test.sh -nthreads 8
-nthreads output directory type seconds
1 local solid state hard disk 126
2 local solid state hard disk 94
4 local solid state hard disk 78
8 local solid state hard disk 74
24 local solid state hard disk 64
4 local normal hard disk 79
4 NFS mounted home disk 94

Page by Oliver Smart and Andrew Sharff original version 28 Nov 2012, revised 5 Dec 2012, updated July 2015. Address problems, corrections and clarifications to buster-develop@globalphasing.com