Cartoon: Helix appearance
Hello,
I observed that Chimera (like almost all other protein viewers) aligns the ribbon of a helix in a way that the ribbon is parallel in every twist (the ribbon virtually forms a cylinder). My question is: is this correct, strictly speaking? I thought that the ribbon should lie in the plane defined by two successive C-alpha atoms and the associated O atom? (Mike Carson defines it that way in his "Ribbons", following the instructions of Richardson's "The anatomy and taxonomy of protein structure"). If you draw it that way, the ribbon forming the helix will tilt slightly outwards. Is the alignment of the helix ribbon in Chimera done simply because it looks better this way or is there another reason?
I did some research on this topic via google and even asked a certified biologist (scientific assistant), but the internet had not much to say about it and the biologist only told me that cartoon drawings don't have to be very accurate, since they are only a tool to get a general idea of the protein's structure.
Best regards, Michael Krone
Hi Michael, Putting aside the philosophical issue of what ribbon orientation has more "truthiness," you can try using the Ribbon Style Editor (under Tools... Depiction): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ ribbonstyle.html
Take a look at the "Residue Class" section. What you get for proteins by default is the "amino acid" definition of - which atoms are mainchain (automatically disappear when you show ribbon): N,CA,C,O - which atom is the "guide" (controls path, smoothed over 5 residues): CA - which atom is the "orientation" atom (controls orientation): O
You can make your own definition and name/save it. Changing the mainchain set does not affect the ribbon appearance at all, so ignore those. I note that O is already the orientation atom. I tried changing the guide atom to N or C, but that didn't seem to tip the ribbon out very much. However, using C and O does make the ribbon plane coincide with those bonds fairly well. (too see this, I made the ribbon wider in the Scaling section of Ribbon Style Editor and opened another copy of the same structure and showed its backbone atoms as sticks)
There is also a "Rotate" option, but the only choice is 90 degrees. Maybe one of the programmers can provide advice on whether it would be easy to edit some number somewhere in the code to get different rotation angles... ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Oct 25, 2007, at 3:47 PM, kroneml@hotmail.de wrote:
Hello,
I observed that Chimera (like almost all other protein viewers) aligns the ribbon of a helix in a way that the ribbon is parallel in every twist (the ribbon virtually forms a cylinder). My question is: is this correct, strictly speaking? I thought that the ribbon should lie in the plane defined by two successive C-alpha atoms and the associated O atom? (Mike Carson defines it that way in his "Ribbons", following the instructions of Richardson's "The anatomy and taxonomy of protein structure"). If you draw it that way, the ribbon forming the helix will tilt slightly outwards. Is the alignment of the helix ribbon in Chimera done simply because it looks better this way or is there another reason?
I did some research on this topic via google and even asked a certified biologist (scientific assistant), but the internet had not much to say about it and the biologist only told me that cartoon drawings don't have to be very accurate, since they are only a tool to get a general idea of the protein's structure.
Best regards, Michael Krone
Hi Elaine,
I didn't know that the ribbon structure/orientation and the guide/orientation atoms can be modified, thank you!
But in fact it's exactly the philosophical issue of what ribbon orientation has more "truthiness" that I'm basically interested in. I'm currently doing some research on cartoon drawings of proteins for my student research project.
Bye, Michael
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, October 26, 2007 1:49 AM To: kroneml@hotmail.de Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Cartoon: Helix appearance
Hi Michael, Putting aside the philosophical issue of what ribbon orientation has more "truthiness," you can try using the Ribbon Style Editor (under Tools... Depiction): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ ribbonstyle.html
Take a look at the "Residue Class" section. What you get for proteins by default is the "amino acid" definition of
- which atoms are mainchain (automatically disappear when you show
ribbon): N,CA,C,O
- which atom is the "guide" (controls path, smoothed over 5
residues): CA
- which atom is the "orientation" atom (controls orientation): O
You can make your own definition and name/save it. Changing the mainchain set does not affect the ribbon appearance at all, so ignore those. I note that O is already the orientation atom. I tried changing the guide atom to N or C, but that didn't seem to tip the ribbon out very much. However, using C and O does make the ribbon plane coincide with those bonds fairly well. (too see this, I made the ribbon wider in the Scaling section of Ribbon Style Editor and opened another copy of the same structure and showed its backbone atoms as sticks)
There is also a "Rotate" option, but the only choice is 90 degrees. Maybe one of the programmers can provide advice on whether it would be easy to edit some number somewhere in the code to get different rotation angles...
Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Oct 25, 2007, at 3:47 PM, kroneml@hotmail.de wrote:
Hello,
I observed that Chimera (like almost all other protein viewers) aligns the ribbon of a helix in a way that the ribbon is parallel in every twist (the ribbon virtually forms a cylinder). My question is: is this correct, strictly speaking? I thought that the ribbon should lie in the plane defined by two successive C-alpha atoms and the associated O atom? (Mike Carson defines it that way in his "Ribbons", following the instructions of Richardson's "The anatomy and taxonomy of protein structure"). If you draw it that way, the ribbon forming the helix will tilt slightly outwards. Is the alignment of the helix ribbon in Chimera done simply because it looks better this way or is there another reason?
I did some research on this topic via google and even asked a certified biologist (scientific assistant), but the internet had not much to say about it and the biologist only told me that cartoon drawings don't have to be very accurate, since they are only a tool to get a general idea of the protein's structure.
Best regards, Michael Krone
participants (2)
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Elaine Meng -
kroneml＠hotmail.de