From: Sibo Lin <sibolin@ca...> - 2009-11-29 20:58:22
I hope this is the correct place to ask this question. I am trying to
overlay a molecular orbital isosurface onto the corresponding molecule
in Jmol, and I have two issues. I am using Jmol 11.8.10, a Jaguar .out
or .xyz file for the atomic coordinates, and Jaguar .plt molecular
orbital isosurface files. I load molecule.xyz, then open the console
editor and enter
isosurface sign red blue "moleculefolder/molecule_MO_110.plt"
1) The orbital is all blue. If I enter the above command a second
time, somehow the signing is picked up, and the orbital remains the
same shape but half of it gets colored red.
2) More crucially, the orbital is not correctly overlaid with the
molecule. It is both smaller and off-center! I tried adding "scale
2.000" or "angstrom" to the above isosurface command, but the size of
the orbital remained the same--too small.
Does anyone have experience loading Jaguar MOs in Jmol? Would I get
more luck if I converted the .plt file to some other isosurface file
format first? Thanks for the help!
Get latest updates about Open Source Projects, Conferences and News.