[chimerax-users] z-slice movie making

Fri Apr 23 11:29:25 PDT 2021

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

> 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 <mailto:vadim.r.kotov at gmail.com>>
>>> To: Stapleton kevin2017/4/3 <kevin.aug at protein.osaka-u.ac.jp <mailto:kevin.aug at protein.osaka-u.ac.jp>>,chimerax-users at cgl.ucsf.edu <mailto: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 <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 <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.
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>>> 
>>> 
>>> 
>>> 
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