[chimerax-users] Making movies and fitting structures into cryoEM

[Elaine Meng]

Dear Madhan,
My previous message already explained how you would move only one model in ChimeraX (you have to select part of it with Ctrl-click and then use the mouse mode "translate selected models" etc.).  For example clicking the "translate selected models" icon in the Right Mouse toolbar assigns this mode to the right mouse button (= trackpad + Alt on Windows, trackpad +  command key on Mac).   See here for which Right Mouse icons go with which functions:
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>

It sounds like even when you are moving everything together, you don't know how to translate models (up, down, left right) in either program.

In Chimera, the default for translation is middle mouse button, or touchpad + option key on Mac (the key may be different on WIndows, just try the ones to the left of the space bar to see which one works).  See the Mouse Preferences (menu Favorites... Preferences, change to category: Mouse) for button assignments:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse>

See also "using touchpad or 1-button or 2-button mouse"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#2button>

In ChimeraX, use command "mousemode" if you want to change assignments.  The "mousemode" manpage linked below also shows a table of the default assignments, e.g. translation is middle mouse button, or Mac trackpad + Alt (or 3-finger drag if multitouch enabled), or Windows trackpad + Ctrl-Alt.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode>

I hope this helps,
Elaine

> On Mar 13, 2020, at 11:28 AM, Tirumalai, Madhan R <mrtirum2 at Central.UH.EDU> wrote:
> 
> Dear Elaine
> 
> Thank you again.
> 
> In Chimera - am able to lock one model by unchecking the "A" box in the Model Panel - in the particular example am working with, its the Cryo-EM density map - the other model is the atomic model from the crystal structure (PDB file) - am not able to move the atomic model  into the Cryo-EM density model. When I use the mouse, all am able to do is rotate the second (atomic) model at the same place - am not able to move it from its location on the screen.
> 
> In ChimeraX - its the same problem and since it does not have the model planel, both models are moving at the same time - the commands are a bit confusing as well
> 
> 
> 
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Friday, March 13, 2020 10:07 AM
> To: Tirumalai, Madhan R <mrtirum2 at Central.UH.EDU>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Making movies and fitting structures into cryoEM
>  
> Dear Madhan,
> I don't understand "not able to lock" in ChimeraX or "not able to move" in Chimera.
> 
> In Chimera, you can control whether each model is hand-movable or not by checking/unchecking the "A" (activated) boxes in the Model Panel, as discussed here:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
> 
> Show the Model Panel from the Chimera Favorites menu.
> 
> By hand you can then move the atomic model to roughly the correct place in the map before optimizing the fit with Fit in Map.  
> 
> The ChimeraX tool Fit in Map is basically the same as the Chimera tool. However, in ChimeraX, the way to move just one model is to select some part of it (Ctrl-click) and then use the mouse mode "move selected models" as discussed in this earlier post:
> <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2017-November/000157.html>
> 
> Also if you additionally press Shift, that mode switches between rotate and translate.
> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.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 Mar 12, 2020, at 6:23 PM, Tirumalai, Madhan R <mrtirum2 at Central.UH.EDU> wrote:
> > 
> > Dear Elaine
> > 
> > Thank you - all those tips were useful.
> > 
> > With ChimeraX, am not able to lock the Cryo-EM density map and then use the crystal structure to fit into it.
> > 
> > Whereas  Chimera allows me to do so - however am not able to move the crystal structure to superimpose on the CryoEM density to do the 'Fit in Map'
> > 
> > is it something am not doing right? I follow these instructions - https://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#fitmodel
> > 
> > 
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Wednesday, March 11, 2020 5:22 PM
> > To: Tirumalai, Madhan R <mrtirum2 at Central.UH.EDU>
> > Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> > Subject: Re: [chimerax-users] Making movies and fitting structures into cryoEM
> >  
> > Dear Madhan,
> > Although ChimeraX doesn't yet have a movie-making dialog (GUI), you can make movies with ChimeraX command scripts.  In a command script (plain text file named ending in .cxc), the "movie" command does recording and creating a movie file, whereas other commands  (show/hide, color, turn, 2dlabel, etc.) can be used to control display, motions, and labeling... whatever you want to happen during the movie.  Simply opening the .cxc file runs the commands.
> > 
> > You can change volume thresholds with the "volume" command "level" option, for example:
> > 
> > volume #1 level 0.08
> > 
> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general>
> > 
> > To gradually change the threshold over multiple display frames, you can combine the "volume" command with the "perframe" command, for example:
> > 
> > perframe "volume #2 level $1" range 0.1,0.3 frames 120; wait 120
> > 
> > (those should be plain text quotation marks, although the e-mail display may change them to fancy quotation marks) 
> > 
> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>
> > 
> > See ChimeraX "making movies" page and links therein:
> > <http://rbvi.ucsf.edu/chimerax/docs/user/movies.html>
> > 
> > ...including movie-making tutorials:
> > <http://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html>
> > <http://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html>
> > 
> > See also general information on ChimeraX command files:
> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files>
> > 
> > For your other question, if you are asking how to fit an atomic structure into a map, see the "Fit in Map" tool and/or "fitmap" command:
> > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html>
> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html>
> > 
> > Or to compare one atomic structure to another atomic structure, you can superimpose them with the "matchmaker" command:
> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>
> > 
> > Chimera has a Matchmaker GUI, but ChimeraX does not have the GUI yet, only the command.
> > 
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > > 
> > >> Begin forwarded message:
> > >> 
> > >> From: "Tirumalai, Madhan R" 
> > >> Subject: ChimeraX
> > >> Date: March 11, 2020 at 1:10:41 PM PDT
> > >> To: "goddard at cgl.ucsf.edu" <goddard at cgl.ucsf.edu>
> > >> 
> > >> Dear Dr. Goddard
> > >> 
> > >> Warm Greetings!
> > >> 
> > >> We have been using ChimeraX to look at mrc files.
> > >> 
> > >> While I am able to use the "Spin movie" option, am not able to use the make movie option, which I could with the Chimera version.
> > >> 
> > >> I would much appreciate if you could kindly let me know how: 
> > >> 
> > >> I can use the movie making option to make movies using different images with increasing/ decreasing thresholds (Volume Viewer)?
> > >> 
> > >> Since am not familiar with docking programs, I would like to know how can one a related crystal structure into a new Cryo-EM structure to show the differences between the crystal structure and the Cryo-Em?
> > >> 
> > >> Thanks
> > >> Madhan