The traditional way of creating the stereochemistry file for O is to edit an existing formatted datablock file, typically the one Alwyn Jones supplies with the program. This is tedious and error prone.
This is a set of M4 macro files that enables you to systematically generate stereochemistry files that include exactly the residue types you are interested in.
In the data directory, files for the individual residue types are stored. In the amino acid entries, the rotamer values are the Duke University rotamers for amino acids [1] (see http://kinemage.biochem.duke.edu/)
Running the Makefile will generate 3 sets of datablock files for O:
$ make
created protein+tRNA.odb
created protein.odb
created stereo_chem_taj.odb
The generated files contain:
- protein.odb -- The standard amino acids with Duke rotamers
- protein+tRNA.odb -- Like above, but includes some tRNA bases
- stereo_chem_taj.odb -- Using Alwyn Jones' rotamer values
Morten Kjeldgaard mok@bioxray.dk Jan 2010.
[1] Lovell, Word, Richardson and Richardson (2000), The Penultimate Rotamer Library. Proteins 40:389-408.