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:

Note: For versions 1.2 and newer, you must download xplor-nih separately, and specify its location during installation of vmd-xplor.

• now based on VMD-1.9.
• added new ``Sausage'' representation where tube width is based on b-factor values.
• ability to SVD fit and visualize dipolar coupling restraints.
• added keyboard shortcuts in the OpenGL window.
• other improvements.

• Intel/Linux - support for kernels 2.4 and newer for x86 and amd64 platforms.
• MacOS X (under an X server).

• 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 NOE info
• used TCL scripting and C++ back-end where necessary. TCL-Tk: fast GUI development.

National Institutes of Health

Department of Health and Human Services