[chimerax-users] ChimeraX bug report submission

5 Jul 2020

      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