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! -Sibo ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
