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

Wed Dec 14 19:59:09 PST 2022

Hi Elaine,
   Thank you for your quick response.
Best,
Jiang

On Wed, Dec 14, 2022 at 7:46 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Jiang,
> The specification is wrong in your torsion command. There should not be
> any ":" before the model number "#1":
>
> >  torsion :#1/A:33 at n,ca,c,o
>
> should instead be something like
>
> torsion #1/A:33 at n,ca,c,o
>
> ... just like in your select command.
>
> I hope this helps,
> Elaine
>
> > On Dec 14, 2022, at 7:35 PM, Jiang Xu <foxjuly at gmail.com> wrote:
> >
> > 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
> > >
> > >
> > > _______________________________________________
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> > > ChimeraX-users at cgl.ucsf.edu
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> > >
> >
>
>
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