[Chimera-users] fivefold rotate command
xucc at wh.iov.cn
Wed Apr 13 06:11:17 PDT 2016
Very nice example. Really big help! Just updated to the newest Chimera version, done!
Thanks again for your time and patience.
> -----Original Messages-----
> From: "Tom Goddard" <goddard at sonic.net>
> Sent Time: Wednesday, April 13, 2016
> To: "Cheng-Chen Xu" <xucc at wh.iov.cn>
> 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.
> > 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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