[Chimera-users] coloring individual segments of a protein

[A G Szabo]

Elaine

I managed to figure out using your instructions and the menus how to color
different sse's of a protein ribonuclease (5RSA). The structure that came up
when I "fetched" it from the PDB had a few of the residues as sticks. Using
the sequence function I was able to select one of the residues, then with
the action menu could hide then sticks of that residue. However, I am not
sure that was the correct way to proceed because when I tried to hide a Phe
residue I was not able to do so.  I have looked at the tutorials that are
available on the site and with due respect I found them to be difficult to
learn from.  

Are there any you tube videos?

So I have a couple of other simple! questions.

If I click on a residue that is visible as sticks is it possible to have the
sticks disappear?

If I click on a residue in the secondary structure, can I make the stick
structure appear?

I will have another look at the tutorials and see if I can figure things
out. I  prefer to use the menu version rather than the command version since
I do not want to have to figure out what all the commands are.


I  am  not really interested in the structure alignment or other similar
features of the program.  I will use the program primarily for preparing
images of secondary structures and highlight selected amino acids as sticks.

Thank you for your assistance.

A. G.  Szabo
Professor Emeritus
Chemistry
Wilfrid Laurier University
Waterloo Ontario Canada.

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: April-17-15 4:33 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] coloring individual segments of a protein

Hello AG,
There are several ways.  I'll try to outline the main ones:

(A) Use the "rainbow command  with the "sse" option to automatically assign
a different color for each secondary structure element (SSE, e.g. helix
and/or strand).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html>

By "automatically" I mean that you don't name each color yourself.  Instead
Chimera interpolates within the specified color range to give each SSE a
separate color.  It doesn't color the coil between SSEs. Example commands
(use Favorites menu to show Command Line):

color gray coil
rainbow sse
rainbow sse orange,white,cyan #0

. where the second example goes through orange, white, and cyan instead of
the default rainbow colors, and only affects model #0 (see command-line
specification
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
).  As explained in the "rainbow" manual page linked above, you could use
"helix" or "strand" instead of "sse" to color only the helices or strands,
respectively. If you don't use any of those, the color will be different for
each residue and gradually change within each SSE.

(B) If you want to control the specific color for each SSE yourself, you
would have to do a separate coloring step for each SSE. You could select the
residues of the SSE and then use Actions. Color in the menu or a command to
color the selection, for example:

color red sel
color purple,r sel
. where the second example ",r" means ribbon-only. 

A convenient way to select an individual SSE is by showing the protein
sequence (menu Favorites. Sequence) and then in the sequence window,
dragging a box to select an SSE.  The light yellow and light green boxes in
the sequence window show where each SSE starts and ends.  

However, if you already knew the residue numbers and were using commands,
you could specify the residues directly instead of selecting them, for
example:

color cyan,r :50-64.A
. to color ribbons-only of residues 50-64 in chain A

Color command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of
Pharmaceutical Chemistry University of California, San Francisco

On Apr 14, 2015, at 7:47 AM, A G Szabo <agszabo at bell.net> wrote:

> How do I use Chimera to color a protein in the following way: for example:
> Helix 1 -  red
> Helix 2 - yellow
> Helix 3 - magenta
> Strand 1 - dark blue
> Strand 2 - cyan
>  
> Etc.
>  
> A G Szabo