Coloring range for residues
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
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
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
participants (2)
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Eric Pettersen -
Ibrahim Moustafa