Rotamer


Introduction

The Rotamer plugin adds side chain conformations to a given residue. It uses a library that has a PDB ATOM record for each atom, with differing residue numbers for separate rotamers of the same residue. Every rotamer coordinate is adjusted to superimpose on the main chain N, CA, and C atoms of the current model of the given residue. Then side chain atom coordinates of every rotamer are added as new models for the atoms of the target residue. Model numbers for new coordinates start from 50.

This plugin does not have a GUI and cannot be started directly, as it requires the target residue as input.

The Default library

The default library is from:

SC Lovell, JM Word, JS Richardson and DC Richardson (2000) "The Penultimate Rotamer Library" Proteins: Structure Function and Genetics 40: 389-408.

Obtained from: http://kinemage.biochem.duke.edu/databases/rotamer.html

Please cite the reference above, when you use the default library.


Configuration file entries

Section Key Valuetype
Description

The library file is in common data directory or user's personal directory (see Config).


For developers

Call Execute( &BODIL::Residue, * ) to add rotamers for that Residue.


Contents