From: MyLinkka (
Date: Wed May 20 2009 - 07:11:35 CDT


After a tryout of the latest version, I think beta 3 is great. However,
I still want to
say some of the 'drawbacks' (or should be better to use 'dislikes') of
vmd. I hope
I would not offend people here.

1. The default colors. In my very personal opinion, the default colors
for atoms
are 'unusual'. Especially, the cyan for carbon atoms, very special. :) I
know no
color is right for a specific atom type. But most of the molecular
program will take 'grey' at default color for carbon. So I think there
is or should
be some convention on this.

2. Python support on windows. I love python and Windows. (this doesn't mean
I don't like Linux. ;) ) I don't intend to compare Windows and Linux
here. But I
wish vmd could support Python scripting on windows. I know there are some
reasons on the website why python is not supported. But as a windows user, I
know 'thousands' of software supporting python scripting out there. Why
cannot vmd?

3. Window layout. I know there is some tradition for L(u)nix software
that many separated
and modeless windows belong to one program. Normally on windows, in this
a program will create some child windows. (if you check what gimpshop
project (and gimp)
does, probably you will understand this. ) Vmd works in the unix way.
But one annoying
thing is, each time when I start vmd, all windows (console, gl and main
window) are overlapped
(at the upper-left corner of my screen). I have to manually move and
rearrange them in
order to see all of them. (maybe this could be controlled in the startup
file?) At this aspect,
other software like pymol does better, it include almost all the
functionalities in one window
(although it has two, but you can input command in the 3d display window
too) and the two
windows are tiled nicely upon startup.

I'm sure above things are not all my 'complaints' about vmd.:) (I will
add more gradually if
you like.) But just because vmd is one of the best molecule
visualization program, I wish it
could be better. Recently, there was a vote for the best molecular
visualization program at
the results are interesting pymol vs vmd 38% to 22%. I think vmd has
many advantages but
loses in default settings, because most of the end users care only about
the quality of image
and user experiences (something different from technique).