VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 19 2002 - 10:29:48 CDT

Hi,
  I've got several answers for your questions.

On Fri, Aug 16, 2002 at 03:48:55PM -0700, Jill Vickery wrote:
> Is there a way to change the default colors used with the charge coloring
> method. I am using version 1.8a21 on Windows XP. I have looked under every
> category in the color menu and cannot find one that changes charge color.
> Under Restype I can change basic and acid but not change in the color used
> with charge.

You can change the color scale that is used for coloring by charge, but
at the present time the range of options are more limited than we would like.
Read about changing color scales in the VMD users' guide and that will help
you get started with this.

> Also I would like to set up some hot keys for stereo on/off on the same
> machine. To test out the command line I need for stereo on/off I tried
> typing "display stereo off" or display stereo scanline interleaved" in the
> terminal window. However, nothing happened and no error message. Has anyone
> else been successful on setting up hotkeys for stereo on/off.

The easiest way to add stereo hot keys is with something like this:
(choice of keys here is arbitrary, you'll want to customize)

user add key u {display stereo CrystalEyes}
user add key i {display stereo {Scanline Interleaved}}
user add key o {display stereo off}

Note that there's an extra set of braces around the "Scanline Interleaved"
text, this is to prevent Tcl from doing weird things since there's a space
in the text.

> Finally, can someone briefly describe how the spaceball works with VMD. I
> read the manual but it is not clear how this actual works. I have seen them
> with the 12 keys and the ball but I would like to know how this is much
> different than a track ball with hot keys or a 5button mouse with 4
> programmable buttons.

The main way in which the Spaceball is different from a mouse or a trackball
with lots of keys, is that the Spaceball provides simultaneous
six-degree-of-freedom motion control. This means that you can apply
pressure on the spaceball in a particular direction, and the molecular
structure you are viewing will move in the direction you push the spaceball.
Similarly, you can apply a torque to the spaceball, and the molecular
structure you are viewing will rotate. The beauty of the spaceball is
that you can effect both translation and rotation operations concurrently,
without any need to switch between modes like you with need to with a mouse
or a trackball. At best, a mouse or trackball can only control 2 axes of
motion at a time whereas the Spaceball can control 6 simultaneously.
This becomes very useful in VMD, since you can then control motions with
your non-dominant hand, leaving the mouse for GUI operations etc.
With some practice one can fly around a molecule using the spaceball
with great ease and precision. Once you get used to using such a
device, its really difficult to go back to just using a mouse. :)

If you're using Windows, VMD also supports the Magellan Spacemouse,
which is a similar device. On Unix, we only have Spaceball support
built-in at the present time, but eventually we'll support both.

Thanks for using VMD,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078