Hi Tom, Very nice example. Really big help! Just updated to the newest Chimera version, done! Thanks again for your time and patience. Chen

-----Original Messages----- From: "Tom Goddard" <goddard@sonic.net> Sent Time: Wednesday, April 13, 2016 To: "Cheng-Chen Xu" <xucc@wh.iov.cn> Cc: Subject: Re: [Chimera-users] fivefold rotate command

Hi Chen,

Yes you can rotate the pentamers of a T=1 icosahedral capsid in Chimera using the “turn” and “sym” commands. The hardest part is figuring out the direction of the 5-fold axis. Here’s an example

open 2bpa open 2bpa sym #1 update true coord #0 # Select opposite pentamers by hand (10 monomers total) with mouse and up-arrow key define axis sel turn a1 5 model #1

I open 2 copies of the virus, the first copy (#0) just serves as a reference coordinate system when I move the second copy (#1). The sym command makes the 60 copies of #1 for the full virus and the “update” option says to update all the positions when copy #1 moves relative to #0. Then I define an axis (called a1) by selecting two opposite pentamers including the #1 monomer. Then I rotate monomer #1 about that axis by 5 degrees, and all the other 60 copies will move automatically to maintain symmetry. Here’s a movie illustrating the motion.

http://www.cgl.ucsf.edu/home/goddard/temp/spin_5fold.mp4

Tom

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On Apr 11, 2016, at 8:42 PM, Cheng-Chen Xu wrote:

Hi Chimera, Is there anyway to rotate each pentamer around its own fivefold axis separately and simultaneously when dealing with a T=1 icosahedral virus capsid? Many thanks,

Chen

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