[Chimera-users] Coloring range for residues

[Ibrahim Moustafa]

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 at cgl.ucsf.edu] 
Sent: Monday, November 09, 2009 7:29 PM
To: Ibrahim Moustafa
Cc: chimera-users at 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

  

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