[chimerax-users] z-slice movie making

Mon Apr 26 03:50:17 PDT 2021

This is awesome and both methods worked out great!  Just what I was looking to do.  

On a personal note, I would like to take this opportunity to say a direct thank you to both you and Dr. Meng.  I always learned so much from both of your responses.  Such a great program and community support.  Thank you.

Hope everyone is having a great day,
Kako

----- Original Message -----
>> From: Tom Goddard <goddard at sonic.net>
>> To: Stapleton kevin2017/4/3 <kevin.aug at protein.osaka-u.ac.jp>
>> Cc: chimerax-users at cgl.ucsf.edu
>> Date: 2021-04-24 03:48:20
>> Subject: Re: [chimerax-users] z-slice movie making
>> 
>> 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.
>> >>>>> _______________________________________________
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>> >>>> 
>> >>>> 
>> >>>> 
>> >>>> 
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>> 
>> 