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|Integration with coot|Copyright
© 2003-2009 by Global Phasing Limited
All rights reserved.
This software is proprietary to and embodies the confidential
technology of Global Phasing Limited (GPhL). Possession,
use, duplication or dissemination of the software is authorised
only pursuant to a valid written licence from GPhL.
The visualise-geometry-coot tool is intended as the principal way of visualising the results of a BUSTER refinement; it provides several lists of different kinds of geometry outliers, which in our experience tend to correspond to places where the model can easily be tweaked to fit better into the density.
You can invoke it either by visualise-geometry-coot when you're in a directory containing a BUSTER refinement, or visualise-geometry-coot <directory name>.
If you close the geometry-outliers window, select 'Geometry issues ...' from the 'BUSTER' menu to reopen it.
Click the 'Start BUSTER' button to start the job. The command-line output from BUSTER will appear in the terminal window from which you started coot, and a progress window will appear which indicates how far BUSTER has got with the refinement.
At the end of the refinement, assuming it's successful, the refined molecule and map are loaded into the coot window
Some users will have coot set up to load extension modules from a particular directory; if you add a link from that directory to $BDG_home/scripts/buster-button.scheme then coot will start by default with the BUSTER menu present.
The present form of the BUSTER button allows you to invoke one of three standard macros: MapOnly, ShortRun and ShortRunVoid. The first of these does not do any refinement, and is appropriate to use on any structure.
But the ShortRun macros turn off a number of the features of BUSTER in order to run more quickly; they are appropriate for doing a small amount of geometry optimisation (if, for example, you have sorted out some misplaced side-chains in a structure, or a dubious conformation of a ligand), but it is not sensible to use the ShortRun macros on structures which have not already been through BUSTER.