C D Schwieters | Search PubMed

PubMed2001

The VMD-XPLOR visualization package for NMR structure refinement.

In this paper we present the VMD-XPLOR package combining the XPLOR refinement program and the VMD visualization program and including extensions for use in the determination of biomolecular structures from NMR data. The package allows one to pass structures to and to control VMD from the XPLOR scripting level. The VMD graphical interface has been customized for NMR structure refinement, including support to manipulate coordinates interactively while graphically visualizing NMR experimental information in the context of a molecular structure. Finally, the VMD-XPLOR interface is modular so that it is readily transferable to other refinement programs (such as CNS).

Bacterial Proteins↗

PubMed2001

Internal coordinates for molecular dynamics and minimization in structure determination and refinement.

We present a software module which allows one to efficiently perform molecular dynamics and local minimization calculations in internal coordinates when incorporated into a molecular dynamics package. We have implemented a reference interface to the NIH version of the X-PLOR structure refinement package and we show that the module provides superior torsion-angle dynamics functionality relative to the native X-PLOR implementation. The module has been designed in a portable fashion so that interfacing it with other packages should be relatively easy. Other features of the module include the ability to define rather general internal coordinates, an accurate integration algorithm which can automatically adjust the integration step size, and a modular design, which facilitates extending and enhancing the module.

Algorithms↗