This is a pymol plugin intended to make working with ribosomal
pdb files easier.  It parses the pdb header and attempts to
make some reasonable inferences about the RNAs and proteins.
It will also attempt to annotate the nearly 150 ribosomal RNA
helices.  Finally, it has some basic functionality to color residues
based upon arbitrary chain or molecule names.

In the 2d directory is a perl script which can color the utexas
ribosomal secondary structure maps.  It does so via the hilariously
crude method of simply inserting color declarations into the original
postscript files.  As such it is not currently very (at all) extensible.


The main thing I would like to do with this code is to have a 2d picture
appear when one selects various helices in the 3d map displaying them in 
both formats.

These files are intended to make working with ribosomal structures easier
to work with.  All functionality is usable via the plugin/ribosome menu
in the python control window.  Most functions in it are also exported to
the pymol command line interface.
The general idea is that one should be able to load a ribosome in the
same manner as remote_pdb_load; but then with little or no effort be
able to identify and work with all of the individual molecules.

In addition, I made an attempt to annotate the small and large subunit
RNA helices for some species including:
Thermus thermophilus, Haloarcula marismortui, Escherichia coli, and
Saccharomyces cerevisiae

These annotations are incomplete and still have some errors.

Finally, I added some functionality which may be used with any pdb file
to color/label individual residues from any molecule by name/number.
This is done by writing a text file with the following format:
# molecule_name
residue_num color_state
The spaces are important.  See data/modification.txt or data/L10.txt
for examples


The following copyright notice is from remote_pdb_load.py, but also lives
in helices.py
# Copyright Notice
# ================
# 
# The PyMOL Plugin source code in this file is copyrighted, but you can
# freely use and copy it as long as you don't change or remove any of
# the copyright notices.
# 
# ----------------------------------------------------------------------
# This PyMOL Plugin is Copyright (C) 2004 by Charles Moad <cmoad@indiana.edu>
# 
#                        All Rights Reserved
# 
# Permission to use, copy, modify, distribute, and distribute modified
# versions of this software and its documentation for any purpose and
# without fee is hereby granted, provided that the above copyright
# notice appear in all copies and that both the copyright notice and
# this permission notice appear in supporting documentation, and that
# the name(s) of the author(s) not be used in advertising or publicity
# pertaining to distribution of the software without specific, written
# prior permission.
# 
# THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
# INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.  IN
# NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
# USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
# OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
# PERFORMANCE OF THIS SOFTWARE.
# ----------------------------------------------------------------------