From: John Stone (
Date: Wed May 20 2009 - 21:11:25 CDT

  I can't address all of your questions until I'm back from travelling
to a conference, but when I return home I can answer several of your
questions and give you solutions for some of the feature requests
you seek, as there are already mechanisms in VMD for handling much of
what you want.

  John Stone

On Wed, May 20, 2009 at 02:11:35PM +0200, MyLinkka wrote:
> Hi,
> 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
> visualization
> 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
> case
> 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).
> ting

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