VMD-L Mailing List

From: Daniel Marin (gethingdone_at_gmail.com)
Date: Tue May 24 2022 - 13:48:54 CDT

Thanks for quick response.

I probably wrongly emphasised "color", while my main concern was "restype"
of Gly. So my question was why VMD considers Gly as a polar..

>From your answer I conclude that I can safely ignore restype assignment and
treat Gly as a hydrophobic if that finds foundation in literature.

Thanks again.
Cheers

On Tue, 24 May 2022 at 15:40, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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)?Ā
> > I am asking because I need to divide amino acids in protein into two
> > groups: hydrophilic and hydrophobic.Ā If Gly is polar, it should be
> > considered as hydrophilic, but, accordingĀ to literature it shouldĀ 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/
>