Re: [chimerax-users] [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@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> <chimera-users@cgl.ucsf.edu <mailto:chimera-users@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
CAUTION: This email was sent from outside of the organization (meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>). Do not click links or open attachments unless you recognize the sender and know the content is safe. If you have any questions, please contact ServiceDesk@vai.org <mailto:ServiceDesk@vai.org> <mailto:servicedesk@vai.org <mailto:servicedesk@vai.org>>.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>
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@sonic.net> Sent: Friday, August 14, 2020 14:52 To: Zheng, Fengwei <Fengwei.Zheng@vai.org> Cc: chimera-users <chimera-users@cgl.ucsf.edu>; ChimeraX Users Help <chimerax-users@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@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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
CAUTION: This email was sent from outside of the organization (meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>). Do not click links or open attachments unless you recognize the sender and know the content is safe. If you have any questions, please contact ServiceDesk@vai.org<mailto:ServiceDesk@vai.org> <mailto:servicedesk@vai.org>. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Tom Goddard -
Zheng, Fengwei