[Chimera-users] Coloring range for residues

[Eric Pettersen]

Hi Ibrahim,
	I'm glad it helped.  I've opened a Trac ticket for your request for  
restricted rainbow coloring, so you'll get a notification when it gets  
implemented.  It could be quite some time before I get to it, though  
if others request it also it could happen sooner.

--Eric

On Nov 9, 2009, at 8:28 PM, Ibrahim Moustafa wrote:

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

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