The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hi, I'm trying to record a movie and the movie generated stops before executing all final steps. It's like the last frames are not recorded even when I see a very high limit. I feel like movie encode starts processing before it is called. For example these commands below are not present in the movie but the movie encode is called afterwards. # Select last interaction area select /F:370,375 /E:270,309,314 show sel atoms hbonds sel select clear # Final show turn x 15 60 rock 130 turn -y 15 60 rock 130 I'm a bit puzzled of why this is happening and I don't really now how to fix it. I attach the .cxc file with the set of instructions that I use to create the movie. Please consider that my experience level is beginner so there could be something that I'm doing wrong. Thank you! Nicco Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX
open "/Users/niar/Dropbox (CRG ADV)/Nicco/projects/06_Chimera/src/movies/6NQ3_Suz12_AS_event.cxc"
open 6NQ3
6nq3 title: Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex [more info...] Chain information for 6nq3 #1 --- Chain | Description A E | Histone-binding protein RBBP4 B F | Polycomb protein SUZ12 C G | PHD finger protein 19 D H | Protein Jumonji Non-standard residues in 6nq3 #1 --- ZN — zinc ion 6nq3 mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly
select all
11928 atoms, 12213 bonds, 30 pseudobonds, 3 models selected
show sel cartoons
style sel stick
Changed 11928 atom styles
hide sel atoms
select /A,B,C,G,D,H
6565 atoms, 6720 bonds, 15 pseudobonds, 3 models selected
hide sel cartoons
select /E
3045 atoms, 3128 bonds, 2 pseudobonds, 2 models selected
color (#!1 & sel) purple
select /F
2318 atoms, 2365 bonds, 13 pseudobonds, 3 models selected
color (#!1 & sel) cyan
select clear
set bgColor white
lighting soft
graphics silhouettes true
view
view name start
movie record supersample 1 size 720,720 limit 5000 directory /Users/niar/Desktop/tmp_chimera pattern Frame_n*
turn z -70
turn x 24
turn y -40
view name hole
wait 5
select sequence EEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLP
1138 atoms, 1174 bonds, 1 model selected
color sel orange
select clear
wait 10
select sequence NHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYT
540 atoms, 552 bonds, 1 model selected
color sel spring green
select clear
wait 10
select sequence GHQKEGYGLSWNPNLSGHLLSASDDHTICLWD
500 atoms, 516 bonds, 1 model selected
color sel spring green
select clear
wait 10
select sequence GHTAVVEDVSWHLLHESLFGSVADDQKLMIWD
512 atoms, 526 bonds, 1 model selected
color sel spring green
select clear
wait 10
select sequence AHTAEVNCLSFNPYSEFILATGSADKTVALWD
488 atoms, 500 bonds, 1 model selected
color sel spring green
select clear
wait 10
select sequence SHKDEIFQVQWSPHNETILASSGTDRRLNVWD
532 atoms, 546 bonds, 1 model selected
color sel spring green
select clear
wait 10
select sequence GHTAKISDFSWNPNEPWVICSVSEDNIMQVWQ
522 atoms, 540 bonds, 1 model selected
color sel spring green
select clear
wait 10
select sequence RKTFKVDDMLSKVEKMKGEQESH
299 atoms, 299 bonds, 1 model selected
color sel red
select clear
wait 10
turn x 20 120 rock 120
wait
turn y 35 150 rock 150
wait
turn y 4 90
wait
turn y 1 50
wait
turn x 1 35
wait
zoom 1.5 80
wait
move x 0.75 15
move y -0.75 15
wait
view name side
select /E:9-28 /E:32-39
239 atoms, 242 bonds, 1 model selected
show sel atoms
hbonds sel
51 hydrogen bonds found
select clear
wait 20
turn x 15 60 rock 60
wait
turn y 15 60 rock 60
wait
~hbonds
select /E:9-28 /E:32-39
239 atoms, 242 bonds, 1 model selected
hide sel atoms
select clear
wait 5
move y 0.75 15
move x -0.75 15
wait
zoom 0.5 80
wait
turn -x 1 35
wait
turn -y 1 50
wait
view hole
move x 0.75 25
move y -0.5 25
wait 25
turn x 0.5 25
zoom 3 80
wait 80
turn x 0.75 25
move y 0.5 25
wait 25
view name zoom1
select /F:129 /E:409 /E:346
31 atoms, 29 bonds, 1 model selected
show sel atoms
color (#!1 & sel) byelement
hbonds sel
12 hydrogen bonds found
select clear
wait 15
turn -y 15 120 rock 120
wait
turn x 15 60 rock 130
wait
wait 15
view name zoom2
turn y -1.5 25
move x -0.5 25
wait 25
turn x -1 25
turn z 1 25
move x 0.4 25
wait 25
select /F:135 /E:285,304,330
34 atoms, 30 bonds, 1 model selected
show sel atoms
color (#!1 & sel) byelement
hbonds sel
11 hydrogen bonds found
select clear
turn y -10 120 rock 180
wait
turn x 15 120 rock 120
wait
wait 20
view name zoom3
zoom 0.5 50
turn -y 1 150
wait
move x 0.75 15
wait
turn x 1 20
wait
zoom 1.5 50
select /F:370,375 /E:270,309,314
42 atoms, 37 bonds, 1 model selected
show sel atoms
hbonds sel
8 hydrogen bonds found
select clear
turn x 15 60 rock 130
turn -y 15 60 rock 130
movie status
\-----Movie status------------------------------ Recording 1785 frames (in 'PPM' format) saved to directory '/Users/niar/Desktop/tmp_chimera' using pattern 'Frame_n*' . Est. movie length is 74.375s. \------------------------------------------------
movie encode /Users/niar/Desktop/Suz12_test1.mp4 format h264 quality low wait true verbose false
Movie saved to /Users/niar/Desktop/Suz12_test1.mp4 executed 6NQ3_Suz12_AS_event.cxc OpenGL version: 4.1 INTEL-14.4.23 OpenGL renderer: Intel(R) Iris(TM) Graphics 6100 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro12,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2,7 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB Boot ROM Version: 189.0.0.0.0 SMC Version (system): 2.28f7 Software: System Software Overview: System Version: macOS 10.15.3 (19D76) Kernel Version: Darwin 19.3.0 Time since boot: 1 day 20:31 Graphics/Displays: Intel Iris Graphics 6100: Chipset Model: Intel Iris Graphics 6100 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x162b Revision ID: 0x0009 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal HP LP2065: Resolution: 1600 x 1200 (UXGA - Ultra eXtended Graphics Array) UI Looks like: 1600 x 1200 @ 60 Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: CNG70302V3 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: 6NQ3_Suz12_AS_event.cxc
Hi Nicco, That's a pretty good start! It always takes a lot of trial and error to make a complicated movie script. I CC'd the chimerax-users@cgl.ucsf.edu list (recommended for asking ChimeraX questions) but did not include your detailed script in case you wanted to keep it private. ChimeraX does not automatically wait until each command is done before starting the next, so perhaps it is racing ahead to the encoding while previous commands are still executing. It's always a little confusing (at least to me) when a "wait" command is needed, so when there seems to be missing content I usually just keep adding "; wait" at the end of each line or to be even more sure, "; wait N" (where N is number of frames) after any multi-frame commands. I suspect you need more wait commands in the last part of your script, say after the last H-bond calculation and/or the two last turn commands. Other tips for your movie: (1) The soft lighting isn't great for ribbons and sticks, it makes them look smudgy or sooty. It is mainly for surfaces/space-filling displays. Instead "light simple" or even "light gentle" may look better. (2) in some cases you can avoid making selections and simply instead name the set of atoms and then use the name in the commands. For example, instead of this select /E:9-28 /E:32-39 show sel atoms hbonds sel select clear ... you could have this name myres /E:9-28,32-39 show myres atoms hbonds myres (3) you can gradually restore a view over a number of frames instead of abrupt transition, for example, instead of view side; wait view hole ... you could transition gradually over 60 frames with view side; wait view hole frames 60; wait 60 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 5, 2020, at 11:27 AM, Nicco <arecco.niccolo@gmail.com> wrote:
The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hi,
I'm trying to record a movie and the movie generated stops before executing all final steps. It's like the last frames are not recorded even when I see a very high limit. I feel like movie encode starts processing before it is called.
For example these commands below are not present in the movie but the movie encode is called afterwards. # Select last interaction area select /F:370,375 /E:270,309,314 show sel atoms hbonds sel select clear
# Final show turn x 15 60 rock 130 turn -y 15 60 rock 130
I'm a bit puzzled of why this is happening and I don't really now how to fix it.
I attach the .cxc file with the set of instructions that I use to create the movie. Please consider that my experience level is beginner so there could be something that I'm doing wrong.
Thank you! Nicco
Hi Elaine, OMG! Thanks you so much! Adding 2 waits at the end of the script solved my issue! Also thanks for the other professional tips, especially lighting and moving are so much nicer! So in the future it is better to write to chimerax-users@cgl.ucsf.edu for any issue I should encounter? Thanks a lot! Nicco
On 6 Jul 2020, at 23:08, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Nicco, That's a pretty good start! It always takes a lot of trial and error to make a complicated movie script. I CC'd the chimerax-users@cgl.ucsf.edu list (recommended for asking ChimeraX questions) but did not include your detailed script in case you wanted to keep it private.
ChimeraX does not automatically wait until each command is done before starting the next, so perhaps it is racing ahead to the encoding while previous commands are still executing.
It's always a little confusing (at least to me) when a "wait" command is needed, so when there seems to be missing content I usually just keep adding "; wait" at the end of each line or to be even more sure, "; wait N" (where N is number of frames) after any multi-frame commands.
I suspect you need more wait commands in the last part of your script, say after the last H-bond calculation and/or the two last turn commands.
Other tips for your movie:
(1) The soft lighting isn't great for ribbons and sticks, it makes them look smudgy or sooty. It is mainly for surfaces/space-filling displays. Instead "light simple" or even "light gentle" may look better.
(2) in some cases you can avoid making selections and simply instead name the set of atoms and then use the name in the commands. For example, instead of this
select /E:9-28 /E:32-39 show sel atoms hbonds sel select clear
... you could have this
name myres /E:9-28,32-39 show myres atoms hbonds myres
(3) you can gradually restore a view over a number of frames instead of abrupt transition, for example, instead of
view side; wait view hole
... you could transition gradually over 60 frames with
view side; wait view hole frames 60; wait 60
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 5, 2020, at 11:27 AM, Nicco <arecco.niccolo@gmail.com> wrote:
The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hi,
I'm trying to record a movie and the movie generated stops before executing all final steps. It's like the last frames are not recorded even when I see a very high limit. I feel like movie encode starts processing before it is called.
For example these commands below are not present in the movie but the movie encode is called afterwards. # Select last interaction area select /F:370,375 /E:270,309,314 show sel atoms hbonds sel select clear
# Final show turn x 15 60 rock 130 turn -y 15 60 rock 130
I'm a bit puzzled of why this is happening and I don't really now how to fix it.
I attach the .cxc file with the set of instructions that I use to create the movie. Please consider that my experience level is beginner so there could be something that I'm doing wrong.
Thank you! Nicco
Hi Nicco, Yes, we recommend using that e-mail address for ChimeraX questions and suggestions, unless you need to include some information that needs to be kept private. You can sign up to be a member of the list (see link below) to send questions instantly and see other people's messages, or even if you are not a member, send questions with slight delay for approval by the moderator. If you get a bug/error, however, it is better to use the menu: Help... Report a Bug. The ways to contact us are described on this page: <http://www.rbvi.ucsf.edu/chimerax/docs/contact.html> You don't need to also CC me, I'm already on that list along with the other developers. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 8, 2020, at 7:09 AM, Niccolò Arecco <arecco.niccolo@gmail.com> wrote:
Hi Elaine,
OMG! Thanks you so much! Adding 2 waits at the end of the script solved my issue! Also thanks for the other professional tips, especially lighting and moving are so much nicer!
So in the future it is better to write to chimerax-users@cgl.ucsf.edu for any issue I should encounter?
Thanks a lot! Nicco
On 6 Jul 2020, at 23:08, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Nicco, That's a pretty good start! It always takes a lot of trial and error to make a complicated movie script. I CC'd the chimerax-users@cgl.ucsf.edu list (recommended for asking ChimeraX questions) but did not include your detailed script in case you wanted to keep it private.
ChimeraX does not automatically wait until each command is done before starting the next, so perhaps it is racing ahead to the encoding while previous commands are still executing.
It's always a little confusing (at least to me) when a "wait" command is needed, so when there seems to be missing content I usually just keep adding "; wait" at the end of each line or to be even more sure, "; wait N" (where N is number of frames) after any multi-frame commands.
I suspect you need more wait commands in the last part of your script, say after the last H-bond calculation and/or the two last turn commands.
Other tips for your movie:
(1) The soft lighting isn't great for ribbons and sticks, it makes them look smudgy or sooty. It is mainly for surfaces/space-filling displays. Instead "light simple" or even "light gentle" may look better.
(2) in some cases you can avoid making selections and simply instead name the set of atoms and then use the name in the commands. For example, instead of this
select /E:9-28 /E:32-39 show sel atoms hbonds sel select clear
... you could have this
name myres /E:9-28,32-39 show myres atoms hbonds myres
(3) you can gradually restore a view over a number of frames instead of abrupt transition, for example, instead of
view side; wait view hole
... you could transition gradually over 60 frames with
view side; wait view hole frames 60; wait 60
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 5, 2020, at 11:27 AM, Nicco <arecco.niccolo@gmail.com> wrote:
The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hi,
I'm trying to record a movie and the movie generated stops before executing all final steps. It's like the last frames are not recorded even when I see a very high limit. I feel like movie encode starts processing before it is called.
For example these commands below are not present in the movie but the movie encode is called afterwards. # Select last interaction area select /F:370,375 /E:270,309,314 show sel atoms hbonds sel select clear
# Final show turn x 15 60 rock 130 turn -y 15 60 rock 130
I'm a bit puzzled of why this is happening and I don't really now how to fix it.
I attach the .cxc file with the set of instructions that I use to create the movie. Please consider that my experience level is beginner so there could be something that I'm doing wrong.
Thank you! Nicco
participants (3)
-
Elaine Meng -
Nicco -
Niccolò Arecco