[chimerax-users] Color atoms by kdHydrophobicity

Tue Aug 30 12:17:56 PDT 2022

Thanks all. Eric, the script works great and I see that it's easy to add
whatever commands I want in there. Excellent.

____________________________

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

On Tue, Aug 30, 2022 at 1:45 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Dan,
> I have fixed Color Actions so that the targeting checkboxes apply to "by
> hetero" etc. and not just the simple coloring buttons.  The fixed version
> will be available in tomorrow's daily build.
> We have a ticket open for executing custom commands after models open (
> #4748 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4748#comment:4>)
> and I've added you to the recipient list for that.  In the interim, I wrote
> some simple Python code to execute "lighting soft" after any model is
> opened.  I attached the file below, and if you add "open
> wherever-you-put-the-attached-file" to the commands that ChimeraX executes
> at startup then you should have the soft lighting you like.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Aug 30, 2022, at 7:57 AM, Daniel Gurnon via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> 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
>> >
>>
>> <Screen Shot 2022-08-29 at 11.30.05 AM.png><Screen Shot 2022-08-29 at
>> 11.30.27 AM.png>
>>
>> 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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