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.
Charles D. Schwieters and
G. Marius Clore,
``The VMD-XPLOR Visualization Package for NMR Structure Refinement,''
J. Magn. Res., 149, 239-244 (2001)
current version: 1.17
Version 1.14 or higher is required when using with Xplor-NIH version
3.0 or newer.
For versions 1.2 and newer, you must download
separately, and specify its location during installation of vmd-xplor.
Supported Hardware Platforms
- based on VMD-1.9.3.
- molWid now supports multiple representations and grouping
structures for group operations (e.g. setting the color of a subset
- better support for multi-monitor setups
- improved keyboard shortcuts.
- noeWid now supports ASSIgn ... OR syntax and center averaging
- by default, each model in PDB files are now loaded as separate structures
- other fixes and improvements.
- Intel/Linux - support for kernels 2.4 and newer for x86 and
- MacOS X (under an X server).
Functionality added to X-PLOR:
Functionality Added to VMD:
- 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++.
- 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
- used TCL scripting and C++ back-end where
necessary. TCL-Tk: fast GUI development.
Thanks to: summer student Devtulya Kavathekar for his work on the most
recent release of VMD-XPLOR.