VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Thu Jul 07 2005 - 11:30:21 CDT

Hi,

   I work with transition metal complexes, and the automatic bond detection does not create visible bonds for coordinate covalent metal-ligand bonds, which are longer than the thresholds. I use VMD to (among other things) visualize intermediate structures in optimizations, which are generally easiest to output as XYZ files, i.e. no connectivity information. There doesn't seem to be a means to save or create user-drawn bonds into a VMD state file--I've tried to see what happens when drawing bonds using "logfile console", but this just reports "label add Atoms 0/x" whether the mouse is in add/remove Bonds mode or not.

   Is there a scripting command in VMD to toggle on add/remove bonds mode, such that a subsequent series of "label add Atoms 0/X" commands could be issued to automatically create user-defined bonds? Or better yet, just to define bonds directly without creating a PSF file?

Thanks,

Chris

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007