Manually producing cluster files

Cluster files are a pseudo pdb file that abstracts a section of difference map. Cluster files can be displayed using the visualise-rhofit-coot visualiser. It should be rare for you to have to produce cluster files manually as, in general, rhofit will produce reasonable cluster files itself. If rhofit does not fit into the site you expect then do try the rhofit option -allclusters and also check the difference density and water in the active site and see the FAQ on rhofitFAQ_refine_for_rhofit.

The prep_rhofit tool can be used to produce cluster files. For help on this type

prep_rhofit -h 

It is typically run:

prep_rhofit -p refine.pdb -m refine.mtz -V <vol>

where <vol> is the required cluster volume in A^3, try 50 Angstroms-cubed

prep_rhofit will output files cluster.lis (listing the names of the x clusters it found) and a pdb file for each cluster (cluster_x.pdb)

Then, re-run rhofit with either

rhofit -l ligand.cif -m refine.mtz -p refine.pdb -C cluster.lis -d output

to tell rhofit to look in all of the found clusters, or

rhofit -l ligand.cif -m refine.mtz -p refine.pdb -c cluster_x.pdb -d output

to tell rhofit to look at a specific cluster.

Page by Tom Womack original version 5 November 2009, Updated 1 April 2010. Address problems, corrections and clarifications to