BUSTER Output Interpretation

  • BUSTER is now exclusively run through the autoBUSTER refine command. However, most of the output routines are those created for BUSTER-TNT and the BUFFET interface when the program was run through a web interface. A great deal of output is produced and it is easy to missing potentially important information. We are currently working on making BUSTER much better at reporting in a condensed sensible fashion.
  • With the current (Feb 2011) release of BUSTER, you are recommended to use the following check list to examine BUSTER refine output:

1. Examine the refine log file

  • Always capture the standard output of refine to a log file. Look at the log file for
    • WARNING messages
    • rms bond and deviation
    • Rwork and Rfree

2. reciprocal-space correlation coefficient plot

3. Rwork/Rfree vs cycle graph

  • run the script
       % graph_autobuster_R -launch -d refine.dir
    • here refine.dir is the results directory as specified by refine -d option
    • it will launch plotmtv (so this needs to be in your path); needs X11
    • the use of the script is illustrated in Student level introduction to autoBUSTER tutorial:
    • for instance (partC) a long refinement of the initial MR model produces a graph like: AutoBusterExampleIntro/partC_graph_autobuster_R.png
  • note that the script will also work while a refine job is running - so can be used for giving progress reports

4. visualise-geometry-coot

  • this is a useful way of quickly launching coot to the view the results of a BUSTER refinement. The procedure is to run the following command:
       % visualise-geometry-coot refine.dir
  • BUSTER produces geometry type screen output where the worst geometry restraints are listed in a text file. The files can be dug out the refine -d results directory but are long lists. visualise-geometry-coot takes this information and produces lists of the worst violators. You can click down the list and be taken in coot to the spot. coot can then be used to correct the model.
  • In addition all the normal coot Validate options can be used.
  • note that the script will work for running refine jobs after big cycle 1 is completed, presenting the model and maps from the last complete big cycle.

Page by Oliver Smart and Tom Womack 06 Feb 2011. Any questions regarding our software or this wiki should be directed to buster-develop@globalphasing.com