From: Sangkha Borah (
Date: Fri Mar 04 2016 - 13:55:43 CST

Dear all,

          I have a situation in which I need to identify random
atoms/molecules (not same set of indices) and print them out with some
other names like X, Y, Z etc. I can identify easily those indices at every
frame using vmd tools, based on distance/angle criteria and print them out
separately, but it will not serve my purpose. Instead I want to keep all
the atoms in the trajectory and only rename the particular selected atoms
only, keeping all the other informations unchanged.
          I think I have to use "rename" command in vmd, but I am not able
to figure out how to use it! Perhaps if I use a selection to rename, it
will preserve the information and rename those chosen indices of atoms for
the frames to follow as well. I certainly do not want to do that.

            Is there any other ways as well that might be useful ? Please
Thank you very much in advance.

Best regards,

Sangkha Borah
IIT Guwahati, Assam, India