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, 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 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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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@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@gmail.com mailto:vadim.r.kotov@gmail.com> To: Stapleton kevin2017/4/3 <kevin.aug@protein.osaka-u.ac.jp mailto:kevin.aug@protein.osaka-u.ac.jp>,chimerax-users@cgl.ucsf.edu mailto:chimerax-users@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.ht... 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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

---

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Hi Kako, Here's another example but with tilted slab. I used mouse modes to set the slab position interactively, which automatically shows the corresponding commands in the Log so that you can use them in a script.

I generated a test map #2 with commands:

open 2gbp molmap protein 5 grid 1

... turned on "tilted slab" mode:

volume #2 style image imageMode tilted

... and then alternated between those two mouse modes mentioned above to get it in the right orientation (turn on each mode by clicking its icon in the Right Mouse toolbar, the "planes" one is a gray plane with straight arrow and "tilted slab" a gray plane with curved arrow). Looking in the Log after I used the mouse I figured out how to specify the desired tilted slab orientation, position, and thickness in a command:

volume #2 tiltedSlabAxis 0.6406,0.2963,-0.7084 tiltedSlabOffset -14.3 tiltedSlabPlaneCount 5

... and then using the "planes" mouse mode I figured out the starting and ending positions of the slab, e.g. commands

volume #2 tiltedSlabOffset -30 volume #2 tiltedSlabOffset 10

... and then you can script gradually changing between those slab positions using the perframe command, e.g.

perframe "volume #2 tiltedSlabOffset $1" range -30,10 frames 200

You can hide the white box outlines with:

volume #2 showoutline f

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

P.S. all the commands have help pages https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands

On Apr 23, 2021, at 11:29 AM, Tom Goddard goddard@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

<planes.cxc>

...

On Apr 23, 2021, at 3:54 AM, Stapleton kevin2017/4/3 kevin.aug@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@gmail.com To: Stapleton kevin2017/4/3 kevin.aug@protein.osaka-u.ac.jp,chimerax-users@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, 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 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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

Thanks for your kind words! We try :-)

Elaine

On Apr 26, 2021, at 3:50 AM, Stapleton kevin2017/4/3 kevin.aug@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@sonic.net To: Stapleton kevin2017/4/3 kevin.aug@protein.osaka-u.ac.jp Cc: chimerax-users@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@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@protein.osaka-u.ac.jpmailto:kevin.aug@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@gmail.com mailto:vadim.r.kotov@gmail.com> > To: Stapleton kevin2017/4/3 <kevin.aug@protein.osaka-u.ac.jp mailto:kevin.aug@protein.osaka-u.ac.jp>,chimerax-users@cgl.ucsf.edu mailto:chimerax-users@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.ht... 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.htmlhttp://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@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > > >

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