On 21:12 Wed 01 Apr , John Badger wrote: > We are examining alternatives for water-picking that workable in the > context of automated refinement and are not aware of any other > incompatibilities at this time.
No doubt you're already aware of findwaters, which comes with coot and
looks like it can be run in an automated fashion:
Usage: /usr/bin/findwaters-real --pdbin pdb-in-filename --hklin mtz-filename
--f f_col_label --phi phi_col_label --pdbout waters-filename --sigma
sigma-level --flood --chop
--mapin ccp4-map-name can be used instead of --hklin --f --phi
where pdbin is the protein (typically)
and pdbout is file for the waters.
The default sigma level is 2.0
Use --chop to remove waters below given sigma-level
In this case, pdbout is the modified input coordinates
Use ---flood to fill everything with waters (not just water peaks)
--
Thanks,
Donnie
Donnie Berkholz
P. Andrew Karplus lab
Oregon State University
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