Rotamers for O Home Page: Richardsons' Laboratory Updated 11/2001


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 as an O database, and this document discusses the use of that database.

To Use

  1. Download the tar file from our web or ftp site.
    We have two O rotamer database files. Both are in one file, rotsForO.tar.Z . The tar file can be downloaded via your browser from either the web site - rotamer section or by maneuvering through the FTP site hierarchy: pub/datasets/rotamer.
    Or, if you prefer, use "anonymous" login to the FTP site.


  2. Extract the files from the tar file.
    These commands will work:

    uncompress rotsForO.tar.Z
    tar -xvf rotsForO.tar
    cd rotsForO


  3. Copy the appropriate database to the O data directory.
    Depending on the version of O which you use, the rotamer database filename is either rscnew.o (version 6 or 7) or stereochemduke.odb (version 8).
    If you are using the rscnew.o file, you'll want to first copy/move the current rotamer database, named rsc.o, to another filename to make a backup copy. Then copy rscnew.o to rsc.o in your O data directory.
    NOTE: as of O v7.0, all non-binary database files should be called .odb. If you have problems with the above instructions with post v7.0, try renaming to rsc.odb, rather than rsc.o
    For version 8, copy stereochemduke.odb to your O data directory.


  4. Read the new rotamer database into your molecule's O file.
    Start up O and load your molecule's database.
    For O pre-8, use the lego_side_chain setup routine to read in the new rotamer library.
    For 0v8, either read in stereochemduke.odb as part of the startup routine, or use a O> read stereochemduke.odb command.


Comments

This file was 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.

Firstly, although the most common rotamer comes first, subsequent 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.

Secondly, 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.

Thirdly, 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 their frequency listed as 0%.

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
[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

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

e-mail:
Bryan Arendall or
David C. Richardson
URL: http://kinemage.biochem.duke.edu
Biochemistry Department
Duke University
Durham, NC USA 27710