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@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
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