Versions of RSRef
The core modules of RSRef2.0 and RSRef2000 are nearly identical in their
calculation of the fit of an atomic model to an electron density map, and the
derivatives need to optimize the fit.
The versions run as modules to different refinement packages:
- RSRef2000 runs as a module for CNS,
supporting simulated annealing or least-squares optimization with Cartesian or
torsion angle parameterization of the model.
- RSRef2.0 runs as a module for TNT,
supporting least-squares refinement with Cartesian model parameterization.
They overlay on top of either CNS
or TNT which must be licensed
and installed before RSRef can be run.
The versions differ in their support that users can expect:
- RSRef2000 is the version most recently developed, and is better
known by those currently developing the software.
- RSRef2.0 has been deployed at many sites over several years and is
more stable, but current personnel have less experience with it and may be
less able to address questions.
Features supported by both versions:
- Local refinement of structure fragments, as well as entire structures;
- Refinement within the molecular graphics program O;
- Refinement against data from x-ray crystallography, or electron microscopy
(the EM feature of RSRef2000 is newly added and undergoing testing);
- Non-crystallographic symmetry;
- Refinement of positions, B-factors and occupancies.
User-interfaces differ substantially:
- RSRef2000 uses Tk and Python menus and windows, run on the local
computer with support for many platforms.
- RSRef2.0 uses Web-based forms hosted either on our web server, or
preferably mirrored on your own site. This can be challenging to set up
for those not familiar with setting up web servers.
The information entered by through the two interfaces is similar, but the
mechanics of how it is used to control program execution are completely
Hardware & Operating System Support
MICHAEL S. CHAPMAN / ERIC BLANC /
ANDREI KOROSTELEV; Last updated
- RSRef2000 is distributed as source. Although tested only on
alphas running OSF unix and silicon graphic Irix 6.x,, the refinement could,
in principle be compiled for any machine supported by CNS. The user
interfaces can also be used on a local graphics computer (PC, unix
workstation), downloading coordinates to, and controlling refinement on a
- RSRef2.0 is distributed as compiled executables for alphas running
OSF unix and silicon graphic Irix 6.x.