vmd-xplor NMR Visualization
The vmd-xplor package is a combination of the X-PLOR structure
determination program and
VMD (Visual Molecular Dynamics)
- a freely
available molecular visualization program. This
package allows manual manipulation of the protein structures to
satisfy experimental NMR data, and can also be used to visualize the
goodness of fit of a particular model to given restraints.
Reference:
Charles D. Schwieters and
G. Marius Clore,
``The VMD-XPLOR Visualization Package for NMR Structure Refinement,''
J. Magn. Res., 149, 239-244 (2001)
.
To obtain this package, visit the
download
page.
current version: 1.5
Note:
For versions 1.2 and newer, you must download
xplor-nih
separately, and specify its location during installation of vmd-xplor.
New features:
- now based on VMD-1.8.5.
- other bug fixes.
Supported Hardware Platforms
- Silicon Graphics Irix6
- Intel/Linux - support for kernels 2.4 and newer for x86 and
amd64 platforms.
- MacOS X (under an X server).
Functionality added to X-PLOR:
- language extensions: small module added.
- remote execution of X-PLOR. Threaded for simultaneous
calculation and communication.
- communicates molecular structures, animation sequences, etc.
to VMD via the tcl-DP sockets package.
- X-PLOR is written in Fortran, extensions in C++.
Functionality Added to VMD:
- easy-to-use molecule display list
- toggling molecule on/off
- quickly focus on molecule of interest.
- change molecule properties
- allows large number of simultaneous structures
- edit tool
- rotate, translate one structure relative to another
- fit to another structure
- change torsion angles
- detect collisions with other molecule
- display NOE restraint information as lines.
- dynamically updated as molecule is edited.
- allows inter- or intra-molecular NOEs
- select a subset of restraints to view
- text annotations displayable
- text view of violations
- display torsion-angle restraints - same functionality as for
NOE info
- used TCL scripting and C++ back-end where
necessary. TCL-Tk: fast GUI development.
Sample Screenshot
question/comments? Contact
vmd-xplor@nmr.cit.nih.gov
.