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

[Zheng, Fengwei]

Dear Tom,

You are AWESOME! Very productive and nice function adding! I’m on the edge of my seat! Stay safe and Have a wonderful weekend!

Best Regards,
Fengwei
________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Friday, August 14, 2020 14:52
To: Zheng, Fengwei <Fengwei.Zheng at vai.org>
Cc: chimera-users <chimera-users at cgl.ucsf.edu>; ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] [External] Re: The command like volume zone in X

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.

Tom


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>

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>

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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