Re: [Jmol-users] Bonds not showing in Jmol 11.6 (Angel Herraez)

Folks, Please don't send the entire list digest as part of your reply to the list. Thanks, Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we

[Jmol-users] Vibrations in Jmol

I would like to use the scale factor for vibrations to demonstrate the classical turning points of a vibration. I am not sure how to read the documentation: "Adjusts the scale of the vector independently of the vibration motion" Does a scale factor of 1.0 simply scale each vector by 1.0, or is

Re: [Jmol-users] Bonds not showing in Jmol 11.6 (Angel Herraez)

Thanks, Angel. I checked over the alignment of the pdb data and, though there wasn't anything obviously wrong, deleting some unnecessary data solved the problem. I wonder why Jmol 11.2 was happy with the data as it was, but Jmol 11.4 and 11.6 didn't like it? Thanks again Ewen -Original Mess

Re: [Jmol-users] Electron density maps in Jmol

ok, that's in. I'll upload a version later this morning. These can be saved as JVXL files with a space savings of about 75%. use the OBJ keyword prior to the file name: isosurface OBJ "sample.obj" See attached image. Note that these can be mapped with values from another function, just like "iso

Re: [Jmol-users] Electron density maps in Jmol

One more thing: These files contain multiple surfaces. Just like other isosurfaces, you can select one of them out: isosurface OBJ "sample.obj" 3 In this case, though, if you leave the number out, you get all of them. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. O