[chimerax-users] Color atoms by kdHydrophobicity

[Daniel Gurnon]

Thanks Elaine, this is very helpful.

I played around with what you sent me and although it works great, I
discovered two little issues with Chimera X:

(1) this is really minor, but I love the "soft lighting" setting and wanted
to have that be the default setting in my installation. I figured I could
set "lighting soft" to execute at startup, but for me, loading a new pdb
always changes the lighting back to "simple". After I change it back to
soft lighting it will stay that way when I bring in new pdb files without
closing the original file, but if for instance I type "close all; open
2ZTA", it's back to simple lighting again. Like I said, a minor issue. But
in good ol' Chimera I appreciated that I could set it up just the way I
like it.

(2) In the color actions GUI, the radio buttons for applying color aren't
being incorporated into the command. For example, if I uncheck everything
except atoms/bonds, and then click "color by heteroatom", it runs "color
byhetero", which applies to all.

I had been using 1.3, but I updated to the latest daily build and still
have the same issues.
Dan

____________________________

Daniel Gurnon, Ph. D.
Associate Professor of Chemistry and Biochemistry
DePauw University
Greencastle, IN 46135


On Mon, Aug 29, 2022 at 2:38 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Dan,
> Thanks for using Chimera & ChimeraX in your teaching!
>
> We do plan to have a Render by Attribute tool in ChimeraX, at least for
> the coloring part.  However, it's a rather complicated GUI that we are
> still working on implementing from scratch (since ChimeraX uses different
> toolkits than Chimera).
>
> ChimeraX does already have the command implementation, "color byattribute"
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute>
>
> Although kdHydrophobicity of amino acid residues is not automatically
> assigned as an attribute in ChimeraX, we provide:
>
> (1) a file for loading it as an attribute, e.g. download this file as
> plain text and then use command "open kdHydrophobicity.defattr"
> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/kdHydrophobicity.defattr
> >
>
> ...after which you could color by attribute with the command, or select
> residues based on their attribute values, label by attribute, etc. There
> are examples specifically for kdHydrophobicity here:
> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>
>
> For example, to use the same coloring scheme as in Chimera, command:
>
> color byattribute kdHydrophobicity protein palette
> dodgerblue:white:orangered novalue gray
>
> There are also files for other hydrophobicity scales, in case you're
> interested...
> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html#examples>
>
> (2) A ChimeraX command file (.cxc) that assigns the attribute as name
> "kdh" (could be changed to kdHydrophobicity if you prefer), shows the
> protein molecular surface, and colors it by those values using the same
> color scheme that was used in Chimera.  The result looks somewhat different
> in ChimeraX than Chimera, however, since there are sharper boundaries in
> the molecular surface between the residues.
> <
> https://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc
> >
>
>
> How to use the .cxc file to define a custom preset (i.e. will make an
> entry in the Presets menu):
> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
>
> This .cxc file is just a starting point if you want to do something
> slightly different. You could remove the commands to hide protein atoms and
> show surface, you could change the coloring target to include atoms, etc.
>
> I realize these are more steps in than in Chimera, however.  If you are in
> control of the installation that all the students use, it would work well
> for you to make a custom preset.  However, if they are all using their own
> installations on their own laptops, you could just tell the students to get
> the .cxc file (as plain text) and simply run the script by opening it in
> ChimeraX every time they want to do the coloring.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Aug 29, 2022, at 9:20 AM, Daniel Gurnon via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi all,
> I use Chimera mostly for teaching purposes, and while Chimera X is
> definitely more user friendly for students, there are occasionally things I
> like from the legacy version that I can't find on a menu in the new
> program. One such feature is "Render by attribute". While the mlp command
> can create a lipophilicity surface, when I teach protein folding I like to
> have students visualize all atoms, with residues colored
> by kdHydrophobicity. Is there a simple way to implement this?
>
> Thanks
> Dan
> ____________________________
>
> Daniel Gurnon, Ph. D.
> Associate Professor of Chemistry and Biochemistry
> DePauw University
> Greencastle, IN 46135
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