[chimerax-users] z-slice movie making
Tom Goddard
goddard at sonic.net
Fri Apr 23 11:48:20 PDT 2021
Hi Kako,
It is nice if the movie shows a text label giving the plane number as it flips through. So here is a script that does that.
# 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
2dlabel text "plane number" xpos 0.8 ypos 0.1
# Record movie
movie record size 500,500
perframe "volume #1 plane z,$1 ; 2dlabel #2.1 text $1" range 80,343
wait 264
perframe "volume #1 plane z,$1 ; 2dlabel #2.1 text $1" range 343,80
wait 264
movie encode ~/Desktop/planes.mp4 quality high
Tom
> 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
>
>
>
>
>> On Apr 23, 2021, at 3:54 AM, Stapleton kevin2017/4/3 <kevin.aug at protein.osaka-u.ac.jp <mailto: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.
>>>>> _______________________________________________
>>>>> ChimeraX-users mailing list
>>>>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>>>>> Manage subscription:
>>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>>>>
>>>>
>>>>
>>>>
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