[chimerax-users] no conformation comparison category in ChimeraX1.5 and ChimeraX-daily

[Jiang Xu]

Hi Elaine and Tom,
   Thank you for your suggestions and explanations in detail. I  want to
show my structure in a more intuitive way, even though it may not represent
the true process that happened in liquid. I then have a question about
measuring torsion angles. I have no problem practicing the example in the
tutorial with only one structure. However, when there's
multiple structures,say #1 and #2, how to measure torsion angle correctly?
The following is an example that I got a mistake:
Command: torsion :#1/A:33 at n,ca,c,o
Missing or invalid "atom" argument: invalid atoms specifier
Command: select #1/A:33 at n,ca,c,o
4 atoms, 3bonds, 1residue, 1 model selected
   How to solve this problem?
Thanks,
Jiang


On Wed, Dec 14, 2022 at 6:51 PM Tom Goddard <goddard at sonic.net> wrote:

> While you can try to reduce clashes during a morph using the method Elaine
> suggested, be aware that morphing does not take clashes into account in any
> way say they are extremely common -- usually hundreds or thousands of atom
> pairs clash in a morph -- since it is just interpolating the
> conformations.  It is not intended to be a realistic motion.  It just shows
> the difference between the conformations in an easy to grasp way.
>
>         Tom
>
>
> > On Dec 14, 2022, at 6:15 PM, Elaine Meng via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hello Jiang,
> > (1) It is not that easy to control. You could try adding an intermediate
> structure, e.g. from your first morph, go to some trajectory frame in the
> middle and manually rotate the arginine to a middle position where you want
> it to go, then save that as PDB, then reopen as new model.  Then to create
> a new morph trajectory, you would put that new model between your other two
> models so that the morphing has an additional stage.
> >
> > To rotate bonds before you save the new model, you could use the "bond
> rotation" mouse mode to do it interactively with the mouse/touchpad or the
> "torsion" command to do it with a command (you would probably have to
> experiment and repeat the command several times and maybe rotate more than
> one bond in the arginine sidechain to get it where you want).
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html>
> > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>
> >
> > (2) Morphing creates a new trajectory model.  After you create the morph
> model, you can play it back however you like (go directly to any part, or
> play multiple times, or back and forth) with the "coordset" command.
> Overall rotation is done with "turn" or "roll" command.
> >
> > If you want to make a fancier movie with morphing, normally you would
> just do the morphing once and then save the session, and then use the
> session with a command script that controls what the movie shows, as well
> as "movie record" to start recording after any setup is done and "movie
> encode" at the end to save the movie,  What the movie shows would include
> "coordset" to play back the morphing results, "turn" or "roll" to rotate
> the whole structure, and possibly several other things: showing/hiding,
> displaying title text, changing colors, etc.  See "making movies" and links
> therein to movie-related commands:
> > <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html>
> >
> > Command files:
> > <
> https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files
> >
> >
> > Both of these movie tutorials include morphing:
> > <https://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html
> >
> > <https://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html>
> >
> > It usually takes a lot of trial and error and executing the command
> script over and over (even for me) to get it just how you like it.  To make
> "coordset" and "roll" commands happen at the same time, put them next to
> each other without any "wait" command between them. Example:
> >
> > open 2gbp
> > open 2fw0
> > mm #2 to #1
> > morph #1,2 frames 120 play false
> > turn y -60
> > movie record
> > coordset #3 loop 3 bounce true; roll x 0.5 726; wait 726
> > movie encode ~/Desktop/junk.mp4
> >
> > Several of the commands have lots of options (e.g. loop or bounce in
> coordset command) and you will need to look at their help pages and spend
> some time trying them.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> >
> >
> >> On Dec 14, 2022, at 5:09 PM, Jiang Xu via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >>
> >> Hello Elain,
> >> Thanks for your explanation. I am able to create the movie now. I then
> have two new questions:
> >> 1.Following the morph command, I found an arginine residue rotate in a
> direction that caused clashes with a neighbouring residue in the movement,
> before moving to the final unclashed position. So is there any way to
> control the movement direction of the side chain to avoid possible clashes?
> >> 2. Now I have the morph trajectory, I also want to have the camera
> rotate as the structure moves at the same time. Is it possible?
> >> Thank you,
> >> Best,
> >> Jiang
> >>
> >> On Mon, Dec 12, 2022 at 8:22 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >> Hi Jiang Xuf,
> >> ChimeraX has a "morph" command (not a tool dialog), see:
> >>
> >> <https://rbvi.ucsf.edu/chimferax/docs/user/commands/morph.html>
> >>
> >> Example:
> >>
> >> open 2gbp
> >> open 2fw0
> >> matchmaker #2 to #1
> >> morph #1,2
> >>
> >> I hope this helps,
> >> Elaine
> >> -----
> >> Elaine C. Meng, Ph.D.
> >> UCSF Chimera(X) team
> >> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>
> >>> On Dec 11, 2022, at 8:52 PM, Jiang Xu via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >>>
> >>> Hey Guys,
> >>>   I am new to ChimeraX and just trying to adapt from Pymol to
> ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big
> Sur. I was trying to use the morph method of ChimeraX to record some clips
> for my publication. But I couldn't find the structure comparison tab from
> the tools dropdown list. I've tried the 1.5 and daily build version and I
> couldn't find this tab in both. Any suggestions?
> >>> Thank you,
> >>> Best,
> >>> Jiang Xu
> >
> >
> > _______________________________________________
> > ChimeraX-users mailing list
> > ChimeraX-users at cgl.ucsf.edu
> > Manage subscription:
> > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> >
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20221214/e1bb72b4/attachment.html>