[Chimera-users] Is it possible to make an open-book diagram using Chimera?

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 14 14:33:16 PST 2013


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




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