[Chimera-users] [External] Re: The command like volume zone in X

Tom Goddard goddard at sonic.net
Fri Aug 14 11:52:53 PDT 2020

Hi Fengwei,

  I added the "wobble" command to ChimeraX today that makes a figure 8 motion.  It will be in tonight's ChimeraX builds -- nightly builds are listed at the bottom of the downloads web page.

  The wobble command is just a shorthand for the turn command and the turn command now has two new options: wobble that controls speed and is the number of frames for a complete figure 8, and wobbleAspect that controls the amplitude of the bobbing motion as a fraction of the side to side motion (default 0.3).  The wobble command uses a default cycle of 136 frames per second which at 60 frames/second rendering is a little more than 2 seconds per figure 8.  The wobble command makes the default amplitude 15 degrees.


> On Aug 14, 2020, at 9:37 AM, Zheng, Fengwei  wrote:
> Dear Elaine,
> Got it, Thank you so much for your kind explanation! Stay safe and Have a great weekend!
> Best,
> Fengwei
> From: Elaine Meng 
> Sent: Friday, August 14, 2020 12:34
> To: Zheng, Fengwei 
> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
> Subject: [External] Re: [Chimera-users] The command like volume zone in X
> Hi Fengwei,
> There is a "vop zone" command in Chimera similar to "volume zone" in ChimeraX.  Same function, but the keywords and syntax are different, see
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone>>
> E.g. something like:
> vop zone #2 #0:.a 2
> As for your other question, Chimera has a "precessionTilt" option to the "roll" command, but ChimeraX does not have this option currently.  Looking at this kind of motion makes me feel seasick, so I don't use it in my own work.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html>>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Aug 14, 2020, at 8:43 AM, Zheng, Fengwei wrote:
> > 
> > Dear Developer,
> > I am wodering if there is a command of Chimera can achieve the same function like "volume zone" in ChimeraX? I tried the command "vol zone #2 near #0:.a range 2", but the chimera always said "unknow keyword #2"~
> > Another thing is that I wonder if there is a command of ChimeraX can achieve the same function like "turn z 2 360 precess 20" in Chimera (to achieve the Wobble motion / "wiggle-rock" motion, like nutation in pymol)~
> > The I tried 1.14, 1.15 and the latest daily built versions of Chimera.
> > The ChimeraX version I used is 1.0, Many thanks!
> > Best,
> > Fengwei
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