[chimerax-users] ChimeraX bug report submission

Sun Jul 5 11:27:17 PDT 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

> 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
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