chemtools.outputs.vmd.print_vmd_script_nci(scriptfile, densfile, rdgfile, isosurf=0.5, denscut=0.05)[source]

Generate VMD (Visual Molecular Dynamics) script for visualizing NCI isosurfaces.

Visualizes NCI (non-covalent interactions) isosurfaces subject to the constraint of density(r) < denscut, i.e. low-density, and colored based on the sign(\(\lambda_2\)) \(\rho\).

  • scriptfile (str) – Name of VMD script file to generate.
  • densfile (str) – Name of density cube file.
  • rdgfile (str) – Name of reduced density gradient cube file.
  • isosurf (float, optional) – Reduced density gradient iso-surface to visualize.
  • denscut (float, optional) – Density cutoff used in creating reduced density gradient cube file. Similar to NCIPlot program, reduced density gradient of points with density > denscut will be set to 100.0 to display reduced density gradient iso-surface subject to the constraint of low density.


The script is the same as the one generated by NCIPlot software version 1.0.