From: Axel Kohlmeyer (
Date: Thu May 09 2013 - 09:21:27 CDT

Why not simply canonicalize the file name yourself before calling mol new?

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

-----Original Message-----
From: Christopher MacDermaid <>
Date: Thu, 9 May 2013 09:30:13
To: <>
Subject: vmd-l: molinfo top get filename, dialogue vs. "mol new"


When calling "molinfo top get filename", the filename returned is
different depending on the method in which I choose to load the molecule.

If I use the file browser dialogue, molinfo returns the absolute path,
however if I use the console with "mol new" it returns the relative path:

vmd> mol new ../../../../test/test.pdb

vmd > molinfo top get filename

detrimental in the event that I want to reload the molecule like so and if
I've changed working directories...

proc reload { mol } {
lassign {*}[molinfo $mol get filename] psf dcd
mol delete $mol
mol new $psf type psf waitfor all
mol addfile $dcd waitfor all

Can this be fixed such that "mol new" will set the correct file name to one
that is the absolute path of the loaded files. I realize this may present
complications since mol new can be used to create an empty molecule, but
the behavior regarding the file names is rather unexpected.


Dr. Chris MacDermaid, Postdoctoral Fellow
Institute for Computational Molecular Science
Temple University, Philadelphia, PA