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O screenshot shows misfit Thr and better rotamer

Rotamer Library For O

All-atom contact analysis shows that all published rotamer libraries contain serious van der Waals overlaps [1]. This should not occur as rotamers, being the more common conformations, should have the lower energy states. Using a select database of 240 high resolution, low-clash score [2], low Rcryst structures and then filtering it by B-factor and clash score, we have composed a rotamer library, consisting of 153 conformers, which we think is more faithful to the rotamer concept and will improve accuracy of new structures. The library is available in two O databases, and this document discusses the use of those.


To Install

  1. Download the tar file.
    We have two O rotamer database files. Both are in one file: download arrow rotsForO.tgz 320KB.
  2. Extract the files from the tar file.
    tar -xzf rotsForO.tgz
    should work.
  3. Copy the databases to your O data directory.
    In the tar archive you'll find stereochem_duke10.odb and rsc_duke.odb. These contain the same rotamers, but they are used by different functions in O (see below). Move or copy both to your designated ODAT directory.

To Use

Two O databases have been supplied; their use varies as detailed below.

  • stereochem_duke10.odb
    Beginning with O version 9, and continuing in version 10, Alwyn Jones has been centralizing the molecule/residue description libraries into one file, stereo_chem.odb. Our stereochem_duke10.odb is a copy of his distribution file (dated 050802), with our rotamers substituted for his. (The ASP PSI* torsion description has also been changed to be the same as other amino acid residues.)
    Our stereochem_duke10.odb can be read instead of the default stereo_chem.odb. In the start-up ritual for creating a new molecule dataset, the query and default suggestion occurs:
    O > Stereochemistry file was never loaded
    O > Enter file name [/usr/local/ono/data/stereo_chem.odb]:

    typing stereochem_duke10.odb to this query will load our rotamer database rather than the default. Otherwise, doing a simple read statement from the O command line:
    O > read stereochem_duke10.odb
    will substitute our rotamers into the datasets of an existing molecule. Note that if you've made additions/corrections to the distributed O stereo_chem.odb, then you'll need to modify stereochem_duke10.odb with the same information.
    stereochem_duke.odb appears to work with all the fitting functions except those using the Lego Library (baton, auto_sc and rotamer_to_view).
    With this version 10 of the library, we have added descriptive labels to the rotamer entries, and changed the order sequence in which the rotamers display. See the comments below.
  • rsc_duke.odb
    This library is needed if you use the lego library and its associated functions. It is read in as part of the lego_setup command. The more descriptive labels and new sequence order found in the stereochem_duke10.odb and discussed below DO NOT apply to this library.

Comments

These two libraries were made from a library of 240 structures at 1.7Å resolution or better. Care was taken to remove side chains which had uncertain positions (e.g. high B-factors) or systematically misfit conformations. The citation below [1] describes our methodology, and the advantages of this library over others previously published.

The approach taken in preparing this file differs from that of the standard O rotamer file.

  1. We have attempted to label the rotamer with descriptive information: the rotamer name and its percent occurance. Because O limits the label to six characters (capital letters, at that!), our labels are not fully descriptive for some rotamers. We always use the full rotamer name and if space allowed added the percent occurance. All labels were filled to six characters with an underscore (if names are complete) or an asterisk (if names are not complete). Four tables are available that map the O-labels to the rotamer data: download the pdf version (download arrow rotsInOvers10.pdf 330KB -- included in rotsForO.tgz).
  2. Rotamers are arranged so that neighbors have similar conformations. This allows you to narrow down your choice to a few rotamers which will be next to each other as you turn the dial. The rotamers are ordered in mtp sequence by each torsion going out from the Cα.
  3. It contains many more rotamers. The original O library used only those rotamers with more than 5% occurrence in order to avoid artifacts (although there still were a few). In contrast, we have carefully tested all rotamers and distributions to avoid (we hope) any artifacts. Thus some rare-but-real conformations are included. This means that non- rotameric conformations should be viewed with even more suspicion than before, and never used in disordered surface positions.
  4. It contains some non-rotamers! These are sample points in allowed, well populated, relaxed conformations. They are not, however, local energy minima and thus, strictly, not rotamers. For example, Glu chi3 has a very flat distribution which is populated throughout, so we have included the rotamer at chi3=0 and two sample points at chi3=60 and chi3=-60. There are sample points only for Glu, Gln, Asp, Asn, Phe and Tyr. They all have an O-label beginning with "S" and no occurance percentage is assigned.

More Information

[1] SC Lovell, JM Word, JS Richardson and DC Richardson (2000) "The Penultimate Rotamer Library", Proteins: Structure, Function and Genetics, 40: 389-408   download arrow {PDF,296KB}
[2] Word, et. al. (1999) "Visualizing and Quantifying Molecular Goodness-of-fit: Small-probe Contact Dots with Explicit Hydrogen Atoms", J. Mol. Biol. 285: 1711-1733   download arrow {PDF,1.4MB}

Please send questions and comments to us rather than Alwyn Jones or the O gurus.