Water organizer???

Dave Schuller schuller at indigo2.biomol.uci.edu
Sat Dec 16 16:59:20 EST 1995

In article <4asp39$5po at news.duke.edu>, bussiere at PROBLEM_WITH_INEWS_GATEWAY_FILE (Dirksen Bussiere) writes:
|> I've just finished refining two proteins and, as usual, have the
|> waters pretty much scatter througout the ASU.  Is there any program
|> that will organize reorder the molecules in a better way

after a round of adding/deleting waters, I have been using the Unix "sort"
command to re-order my waters by the X coordinate. something like this:

fgrep WAT junk.pdb |sort +5 -6 -n | pdb_reres -400 |pdb_chain \
|pdb_xseg -WAT |sed -e "s^O   WAT^OH2 WAT^g" >wat.pdb

where "pdb_reres" etc. are utilities to reset the residues numbers and such.
These are available by anonymous ftp from
indigo4.biomol.uci.edu , directory pub/schullersoft .  The "sed" command above
handles differences in naming waters between the graphics program (FRODO) and
the refinement program (Xplor).

              "The gene is the basic unit of selfishness"
                   - Richard Dawkins in The Selfish Gene
                        Dave Schuller
                        University of California-Irvine
                        schuller at indigo2.biomol.uci.edu
                        modern man in a post-modern world

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