Hi Eric,

Thank you very much, as usual, I got the help I expected from chimera team.

Actually, the conformational change for the structure I have is dramatic and involves wide range of residues. It is really painful for the eye to follow the structural change for a certain element. Coloring the residues in few colors did the job; however, the rainbow coloring using the script you sent did a much better job.

It would be useful if this command can be added to the chimera!.

Many thanks,

Ibrahim

--------------------------------------------------------------------------------------------------------------------------

Ibrahim M. Moustafa, Ph.D.

Biochemistry and Molecular Biology Dept.

201 Althouse Lab., University Park

Pennsylvania State University

PA 16802

Tel. (814) 863-8703

Fax (814) 865-7927

From: Eric Pettersen [mailto:pett@cgl.ucsf.edu]
Sent: Monday, November 09, 2009 7:29 PM
To: Ibrahim Moustafa
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Coloring range for residues

Hi Ibrahim,

I'm not 100% sure why you want to rainbow the highlighted part of your structure, rather than use a single color, or color the rest of the structure dark gray, or make the rest of the structure semi-transparent, or many other possible highlighting schemes.

Anyway, there's no way to do it without resorting to (simple) Python. Put the following in a file that ends in ".py":

import chimera

residues = chimera.selection.currentResidues()

residues.sort()

for i, r in enumerate(residues):

r.highlightNum = i+1

Then select the residues you want highlighted in Chimera. Run the Python script by opening it with the "open" command or with the File->Open dialog. Then run this Chimera command:

rangecolor highlightNum,r min blue mid white max red sel

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

http://www.cgl.ucsf.edu

On Nov 9, 2009, at 11:14 AM, Ibrahim Moustafa wrote:

Dear Chimera team,

  I wonder if there is a way to color a certain range of residues using rainbow.
I tried to use the rainbow command with atom_spec but it applied for the whole chain.

What I want to do is to color part of the structure as a rainbow (from blue-white-red) with an increasing order of residues number.
I just wanted to highlight a region of conformational change so the eye can follow which part of the structure has changed dramatically.

  Thanks in advance for your help.

  Ibrahim

--

Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802

Tel. (814) 863-8703
Fax (814) 865-7927

_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users