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April 7, 2020

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WebMO Support Forum » Feature Requests » Features of WebMO Pro v 17 « Previous Next »

Author Message
John Keller
Unregistered guest
Posted on Sunday, August 28, 2016 - 4:13 am:   

Have any capabilities of WebMO Pro v 16 been lost in updating to v 17?
John Keller
Unregistered guest
Posted on Monday, August 29, 2016 - 2:50 am:   

In v 17, how do you export a surface in the .cub or .jvxl format? I'm just not finding it in the new interface.
John Keller
Unregistered guest
Posted on Wednesday, September 21, 2016 - 5:47 am:   

v 17 saves only .cub format surface files. (Surfaces in the very compressed jvxl format can be obtained in Jmol by displaying the .cub surface with an "isosurface" command, then saving it in jvxl format with a "write isosurface name.jvxl" command.)

To use Jmol to display an electrostatic potential map similar to that shown in WebMO, do the following, using the water dimer as an example: Do Geometry Optimization and Molecular Orbital jobs with the B3LYP/cc-pVDZ method and the NWChem engine (job #250472 on WebMO Demo server). Under View Job, save the molecule by File, Export Molecule, PDB format. Set File, Preferences, Isosurfaces, Density to 0.01. Click the "Electron Density" line in the Molecular Orbitals table. Do File, Export Molecule, Cube Format. Click the "Electrostatic Potential" line, and do File Export Molecule, Cube Format.

Rename these files respectively as h4o2-nw.pdb, h4o2-ed-nw.cub, and h4o2-esp-nw.cub.

In Jmol (v 14.4.4), issue the following set of commands:
load h4o2-nw.pdb; background [245,245,245]; isosurface cutoff 0.01 "h4o2-ed-nw.cub" color absolute 1.5 2.4 map "h4o2-esp-nw.cub"; isosurface backlit; isosurface translucent 90; set fontscaling on; label %[atomno]; font label 14 sansserif bold; color label black;

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