From: Norman Geist (
Date: Mon Feb 15 2016 - 00:14:22 CST

Also, you can create a representation of only your desired atom and use Mouse->Move->Rep to move it with drag’n’drop.



Norman Geist


Von: [] Im Auftrag von jing liang
Gesendet: Samstag, 13. Februar 2016 18:16
Betreff: vmd-l: moving atoms and updating distances




I need to introduce one atom in an existing molecule. I load the molecule

and then I load the "guess" coordinates of the extra atom. Then, I check out

the F (fixed) option in VMD for the molecule and only the extra atom is able to move.

After that, I try to compute the distance between the

extra atom and some existing atoms to improve the guess coordinates.


However, it seems that the distances are not updated in VMD using

this procedure. Is there a way to do this manual docking procedure in VMD?