[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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