[chimerax-users] z-slice movie making

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 26 09:30:39 PDT 2021


Thanks for your kind words!  We try  :-)

Elaine

> On Apr 26, 2021, at 3:50 AM, Stapleton kevin2017/4/3 <kevin.aug at protein.osaka-u.ac.jp> wrote:
> 
> 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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