Xtalview rotamer files 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 discussed the use of that database.



To Use

  1. Download the tar file from our web or ftp site.
    The rotamer libraries are in a tar'ed Zipped file named rotsForXView.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/rotamers.
    Or, if you prefer, use "anonymous" login to the FTP site.


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

    uncompress rotsForXView.tar.Z
    tar -xvf rotsForXView.tar
    cd rotsForXView


  3. Copy the database to the XtalView data directory.
    First create a backup copy of the current rotamer libraries, dict.noh.pdb and dict.allh.pdb. Then, copy/move the two new rotamer dictionaries, into the XtalView data directory (typically /usr/local/XtalView/data/ ).


  4. You can now select either of these dictionaries from the "Models" pane of Xfit.



Comments

The rotamer dictionary was made from a database of 240 structures at 1.7Å resolution or better. Care was taken to remove side chains which had uncertain positions (eg 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 rotamer file.

Firstly, although the most common rotamer comes first, subsequent rotamers are arranged so that neighbours 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. We examined all rotamers and distributions to avoid (we hope) artifacts. Thus there are some rare-but-real conformations. This means that non-rotameric conformations should be viewed with even more suspicion than before.

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%.

KNOWN BUGS:
Histidine can have several protonation states. The allh file only allows for one (doubly protonated). This behaviour is the same as the original files provided with XtalView.

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 Duncan McRee.

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