From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 24 2022 - 08:40:01 CDT

Hi,
  VMD initially assigns the vast majority of colors algorithmically,
because different file types use different naming conventions. As such,
you should consider the initial color assignment not much more than an
attempt to assign unique colors to each unique type that VMD finds when
the structure is loaded. Beyond that, if you have a preference to follow
existing practice or literature, you'll want to use the color menu to
change the automatic assignments to follow your preferred scheme.

If you build up sets of colors you like, you can either use simple
scripting, or a tool like the VMD preferences plugin to manage your
preferred color assignments. This will work well if you tend to use
the same file formats with the same atom/residue naming conventions, etc.

Best,
  John Stone

On Tue, May 24, 2022 at 11:28:35AM +0200, Daniel Marin wrote:
> Hi all
> As of my understanding Gly is considered as non-polar amino acid in
> protein (at neutral pH).
> Why, in VMD, its restype color is green (representing it as polar amino
> acid)?┬
> I am asking because I need to divide amino acids in protein into two
> groups: hydrophilic and hydrophobic.┬ If Gly is polar, it should be
> considered as hydrophilic, but, according┬ to literature it should┬ be
> hydrophobic.
> Thanks

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