VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Jul 03 2010 - 09:12:35 CDT

Hi,
  I only have about 2 minutes to write, but I wanted to give you
some quick tips:

On Thu, Jul 01, 2010 at 06:10:10PM -0500, Luis Guillermo Cota Preciado wrote:
> Here's a couple of questions whose answers I haven't been able to come up
> with myself:
>
> * At least on my screen, when VMD is in perspective mode atoms (spheres)
> become oblong as they get closer to the edge of the window. How can I
> correct this
> behavior?

To decrease the perspective effect (the default is similar to looking
through very wide-angle camera lens), do the following steps:
  - in the "Display Settings" menu, change the "screen dist" value
    to "-6" (which will effectively zoom in), and then scale down your
    molecule using the moust, to return it to a normal size. This will
    greatly reduce the perspective foreshortening you see affecting spheres
    at the edge of the screen (making them less egg-shaped).

> * In trying to replicate a color with its RGB values (divided by 255 in
> order to get the fractional number) I find out that I get very
> different results as those wished. Particularly, I am having trouble
> with the yellow-orange range. Also, the "Color Scale" sliders don't
> seem to have any effect on the color of the selected atom type, for
> example. How can I adjust a color's brightness and saturation?

  - You can set the colors in VMD arbitrarily using the "color" text commands
    as described in the user's guide:
      color change rgb 0 1.0 1.0 1.0 (will change blue to white)

    Note that the RGB colors that are used to color the surface are only
    on part of the coloring process. The other part relates to the lighting
    in the scene. To get colors that most closely match what you have
    specified in RGB, you will want to make a new material in the
    "materials" menu. For your special material, you will want to set
    the "diffuse" parameter to 1.0, and leave ambient, specular, etc at 0.0.
    This will give you a surface color that closely matches your original
    RGB color but even in this case, the shading has a strong effect on how
    the color looks on the display.

> * Default (VDW) values for Si and O radii are 2.1 and 1.62 Angstroms,
> respectively, whereas the Si-O bond length is 1.6 Angstroms, approx.
> Even so, the Si-O bond seems to be much larger than the individual
> atoms in the CPK representation, with Sphere Scale set to 1. In other
> words, what is the real scaling factor for atoms in the CPK
> representation? (It is obviously much less than one.)
> Thank you very much in advance.

    - I'll have to lookup the sphere scale for the CPK rep, but it seems
      to me that it's something like 0.3. Use the VDW rep if you want to
      see the full atom sizes.

I've gotta run for now, let us know if you have further questions.

Cheers,
  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