From: Pawel Kedzierski (
Date: Wed Jan 20 2021 - 08:19:46 CST

Dear David,

I guess what you refer to is just the default atom label, which is
completely arbitral; you can label atoms with any text, either via GUI
(Graphics->Labels..., Properties tab) or using Tcl commands
<> (e.g.
"label textformat Atoms 0 { MY OWN ATOM LABEL  }". The default format is
"%R%d:%a" which is substituted with residue name, residue id, colon and
atom name.
However, the residue and atom names are taken from the molecule input
file and they follow the source format
specification.<;!!DZ3fjg!uKWiixlPzN0Ob7jdx3TOBz8fsTRUMO-tdQaQ8QRtFak6R90whu3STlqvs5y8ftwB0Q$ >


> Good day colleagues,
> I have an academical curiosity:
> What was the reason behind the semantic structure of naming atoms in VMD?
> i.e. THR40:HN
> Thank you in advance,
> David