From: Pawel Kedzierski (
Date: Thu Jan 22 2015 - 02:53:57 CST

W dniu 22.01.2015 o 04:47, JhonY. I. pisze:
> Hi,
> I'd like to visualize sodium and chlorine ions in VMD using pdb file.
> I used atom name of Na or sodium for sodium ion but It is visualized
> as if it is nitrogen or sulfur atom.
> It appears that VMD detects the first letter of atom name only.
> How can I solve this problem?
Use a properly formatted PDB file:
The element symbol, in uppercase, should be specified in columns 77-78
of HETATM and ATOM lines.
Other ways include setting the element by Tcl scripting or interactively
using the Molefacture plugin.

BTW, there seem to be a bug in Molefacture in that it ignores the
elements from PDB file (although VMD itself reads them correctly). At
least for me chlorine atoms are considered argons by Molefacture.
However if the element is edited in Molefacture and the molecule saved
as PDB, the resulting PDB does contain proper element symbols.
> Thank you very much for your helps in advance.
> Best
> Young