[chimerax-users] z-slice movie making

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 23 11:59:01 PDT 2021 

Hi Kako,
Here's another example but with tilted slab.  I used mouse modes to set the slab position interactively, which automatically shows the corresponding commands in the Log so that you can use them in a script. 

I generated a test map #2 with commands:

open 2gbp
molmap protein 5 grid 1

... turned on "tilted slab" mode:

volume #2 style image imageMode tilted

... and then alternated between those two mouse modes mentioned above to get it in the right orientation (turn on each mode by clicking its icon in the Right Mouse toolbar, the "planes" one is a gray plane with straight arrow and "tilted slab" a gray plane with curved arrow). Looking in the Log after I used the mouse I figured out how to specify the desired tilted slab orientation, position, and thickness in a command:

volume #2 tiltedSlabAxis 0.6406,0.2963,-0.7084 tiltedSlabOffset -14.3 tiltedSlabPlaneCount 5

... and then using the "planes" mouse mode I figured out the starting and ending positions of the slab, e.g. commands

volume #2 tiltedSlabOffset -30
volume #2 tiltedSlabOffset 10

... and then you can script gradually changing between those slab positions using the perframe command, e.g.

perframe "volume #2 tiltedSlabOffset $1" range -30,10 frames 200

You can hide the white box outlines with:

volume #2 showoutline f

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. all the commands have help pages
<https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands>

> On Apr 23, 2021, at 11:29 AM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Kako,
> 
>   Here is an example script to record a movie flipping through planes.
> 
> # Setup scene.
> # For movie recording I would normally setup by hand and
> # save a session instead of using commands.
> windowsize 500 500
> open 22910 from emdb
> volume #1 style image level -0.4458,0 level 2.326,1 plane z,200
> view orient
> zoom 2
> camera ortho
> 
> # Record movie
> movie record
> volume #1 plane z,80,343
> wait 264
> volume #1 plane z,343,80
> wait 264
> movie encode ~/Desktop/planes.mp4 quality high
> 
> 	Tom
> 
> <planes.cxc>
> 
> 
>> On Apr 23, 2021, at 3:54 AM, Stapleton kevin2017/4/3 <kevin.aug at protein.osaka-u.ac.jp> wrote:
>> 
>> Hello Vadim my new cross-forums friend!
>> 
>> I completely forgot about the view name options!   Yes this worked just fine but with some tweeks to get the video to 10sec.  I couldn't get the 'framerate' command to work properly.  So I just improvised :-)
>> 
>> 
>> For anyone else curious or learning here is how I achieved this:
>> 
>> ## download thetest EM density
>> open 22296 from emdb
>> 
>> ## Selected "clip" button from the "right mouse" tab and slid the clipper view all the way out so it looked as if normal.  This will be my start
>> ## frame.  Then save this snapshot/scene
>> view name 1
>> 
>> ## then use the clip to slide all the way through the volume until a desired point.  In my case all the way through.  Saved this 
>> ## snapshot/scene
>> view name 2
>> 
>> ## go back to original snapshot
>> view 1
>> 
>> ##Test the transition works
>> view 1  1; wait 1; view 2 250; wait 250
>> 
>> ## record the movie
>> movie record  supersample 3; view 1  1; wait 1; view 2 250; wait 250; movie stop; movie encode  ~/Desktop/9.mp4
>> 
>> 
>> I tried the above method and it worked great!  However, now I want to look even cooloer by making the same movie, but with the volume styled in "Plane" or "tilted slab".  
>> 
>> Anyone have a workaround for this?
>> 
>> Thanks again Vadim and next time I'm in the EU I will buy you a beer/coffee!
>> 
>> Kako
>> 
>> 
>> 
>> 
>> 
>> ----- Original Message -----
>>>> From: Vadim Kotov <vadim.r.kotov at gmail.com>
>>>> To: Stapleton kevin2017/4/3 <kevin.aug at protein.osaka-u.ac.jp>,chimerax-users at cgl.ucsf.edu
>>>> Date: 2021-04-23 17:18:14
>>>> Subject: Re: [chimerax-users] z-slice movie making
>>>> 
>>>> Hi, Kako!
>>>> 
>>>>  I think all you have to do is to save respective views with clipping 
>>>> enabled and then make a movie that would interpolate between these 
>>>> views. To be more specific:
>>>> 
>>>> 1) Save the starting view:
>>>> view orient
>>>> view name initial_view
>>>> 
>>>> 2) adjust the clipping planes and orientation of the map as you wish and 
>>>> save another view:
>>>> view name clip_view
>>>> 
>>>> 3) go back to the initial view and interpolate to the clipped view over 
>>>> 100 frames:
>>>> view initial_view
>>>> view clip_view 100; wait 100
>>>> 
>>>>  Of note, I used these commands ~1 year ago to make a movie for our 
>>>> lab's webpage 
>>>> <https://www.cssb-hamburg.de/research/research_groups/loew_group/index_eng.html>, 
>>>> so the syntax might have changed in the meantime.
>>>> 
>>>>  Alternatively, you could set up the clipping planes outside the map 
>>>> and then move it through the clipping planes with move 
>>>> <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> command 
>>>> that uses several frames.
>>>> 
>>>>  Good luck!
>>>> 
>>>> Best wishes,
>>>> Vadim
>>>> 
>>>> 
>>>> On 23.04.21 09:41, Stapleton kevin2017/4/3 wrote:
>>>>> Greeting everyone in the ChiX community.  Long time listener first time caller :-)
>>>>> 
>>>>> I was wondering if anyone could help me with making a movie that is essentially slicing (clipping) through a given volume.
>>>>> 
>>>>> I am pretty comfortable with the movie making movie parameters and I have read through the sections
>>>>> 
>>>>> 1) help:user/movies.html
>>>>> 2) help:user/commands/clip.html
>>>>> 
>>>>> However the command parameters explanation is juuuuust a smidgen beyond my limits (almost there...damn!) and cant seems to get this into a working movie (if possible at all).
>>>>> 
>>>>> So, using the emdb entry: 22910 for example case, how can I make a movie that is 10 seconds long and extends through the clipping plane of a given volume, moving front to back (from the "view orient" perspective; the clipping plane will extend forward through the volume, and back again)
>>>>> 
>>>>> Thanks for all your help in this specific case, and for all of the efforts put into to this mailing list.  It has been a well spring of fun learning for me over the years.  SO many cool tips and tricks to make macro-molecular structures look top notch and cool.   THANKS CHIMERA TEAM!!
>>>>> 
>>>>> All the best and well wishes from Japan,
>>>>> Kako
>>>>> 
>>>>> PS. apologies if this was covered in a previous thread.  I must have missed it.
>>>>> _______________________________________________
>>>>> ChimeraX-users mailing list
>>>>> ChimeraX-users at cgl.ucsf.edu
>>>>> Manage subscription:
>>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>>>> 
>>>> 
>>>> 
>>>> 
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu
>> Manage subscription:
>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

More information about the ChimeraX-users mailing list