Is it possible to make an open-book diagram using Chimera?
Hi - I want to create an open-book diagram showing amino acid interactions present in a buried surface area. I was wondering if it is possible to create these types of diagrams with Chimera without cheating by cutting the protein into two and flipping it. In my experience, it's extremely hard to get things rotated correctly when you do that. Any ideas would be much appreciated. Thank you. Amy Migliori UCSD
Hi Amy, Sorry, there is no automatic function to create such diagrams. I guess I wouldn't call it "cheating," but yes, I believe you would have to split the structure (or equivalently, open twice and delete complementary portions from the two copies), reorient to align the interface, and then perform exact translations and rotations on the separate models using "move" and "turn" (or "roll"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> Although the above allows specifying a center of rotation (so that you could give each structure a center within itself), it might be easier just to use the following first: set independent You can also turn off "perspective" with command: set projection ortho <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> For example, I tried the following: open 3eeb open 3eeb del solvent del #0:.a del #1:.b surf color green #0 & #1 z<5 color green #1 & #0 z<5 [ ... reoriented view to put #1 on left and #0 on right ...] set independent set projection ortho turn y 90 mod 0 turn y -90 mod 1 move x 10 mod 0 move x -10 mod 1 focus I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 14, 2013, at 1:27 PM, Amy Davenport wrote:
Hi - I want to create an open-book diagram showing amino acid interactions present in a buried surface area. I was wondering if it is possible to create these types of diagrams with Chimera without cheating by cutting the protein into two and flipping it. In my experience, it's extremely hard to get things rotated correctly when you do that. Any ideas would be much appreciated. Thank you. Amy Migliori UCSD
Excellent - Thank you for helping me with the specific commands for constrained rotation/translation. When I mentioned "cheating" I was really referring to free-handing the whole thing, which doesn't work very well at all. Have a good one! -Amy On Jan 14, 2013, at 2:33 PM, Elaine Meng wrote:
Hi Amy, Sorry, there is no automatic function to create such diagrams. I guess I wouldn't call it "cheating," but yes, I believe you would have to split the structure (or equivalently, open twice and delete complementary portions from the two copies), reorient to align the interface, and then perform exact translations and rotations on the separate models using "move" and "turn" (or "roll").
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
Although the above allows specifying a center of rotation (so that you could give each structure a center within itself), it might be easier just to use the following first:
set independent
You can also turn off "perspective" with command:
set projection ortho
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html>
For example, I tried the following:
open 3eeb open 3eeb del solvent del #0:.a del #1:.b surf color green #0 & #1 z<5 color green #1 & #0 z<5 [ ... reoriented view to put #1 on left and #0 on right ...] set independent set projection ortho turn y 90 mod 0 turn y -90 mod 1 move x 10 mod 0 move x -10 mod 1 focus
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2013, at 1:27 PM, Amy Davenport wrote:
Hi - I want to create an open-book diagram showing amino acid interactions present in a buried surface area. I was wondering if it is possible to create these types of diagrams with Chimera without cheating by cutting the protein into two and flipping it. In my experience, it's extremely hard to get things rotated correctly when you do that. Any ideas would be much appreciated. Thank you. Amy Migliori UCSD
participants (2)
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Amy Davenport -
Elaine Meng