2007.06.07 -- This application has been archived. Local users, see a CSB staff member for help if you need to run this program in the Core.

Nuclin-Nuclsq Package: A rapid and automatic online refinement tool of partial or full assemblies of nucleic acids.

The three step refinement protocol incorporates canonical as well as noncanonical base pairing constraints together with restraints imposed by covalent geometry, stereochemistry, and van der Waals contacts.

To use the NUCLIN-NUCLSQ package in the CSB core, type the following (on an SGI):

setup nuclsq
(or source /srv/local/setup/nuclsq.set)

You then have the following programs in your path:

prenuc
nuclin
nuclsq
pdb2hd
hd2pdb

the 3-steps refinement programs: prenuc, nuclin, nuclsq
two format conversion programs: pdb2hd, hd2pdb

The online manual contains an overview

The publication of research using this software should reference:
Westhof, E., Dumas, P., & Moras, D. (1985) J.Molec.Biol. 184, 119-145.
Westhof, E., Dumas, P., & Moras, D. (1988) Acta Cryst. 44A, 112-123.