Opened 6 years ago

Closed 6 years ago

#2312 closed defect (can't reproduce)

hide/show confusing

Reported by: yazan.abbas@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-55-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-08-13)
Description
(can't remember if I already reported this bug) Showing cartoons, atoms, surfaces, using either command line or GUI, is not behaving as expected. Sometimes I have to keep fiddling with hiding and showing a component multiple times until the desired compononent shows up. Sometimes I it will hide/show atoms and surfaces, but not cartoons, but after several attempts, the cartoon will eventually show up

Log:
UCSF ChimeraX version: 0.91 (2019-08-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/yazan/Dropbox/Abbas_etal_2019_brainV-
ATPase/Figures/Video1/movie1_190813.cxs

opened ChimeraX session  

> view position #7 sameAsModels #10

> hide #10/K1 target abp

> hide #10/K2 target abp

> hide #10/K3 target abp

> view frame1

> set maxFrameRate 25

> windowsize 1080 1080

> view frame1

> movie record supersample 3

> wait 1

> coordset #10 1,181

> roll 0.133,0.0389,0.989 -1.988950276243094 181 coordinateSystem #10 models
#7 center 160,176,0

> wait 181

> wait 1

> movie stop

> movie encode test.mp4 quality high

Movie saved to test.mp4  
  

> view frame1

Unknown command: regen  

> alias regen close #7; volume zone #4 nearAtoms (#1 & ~#1/s1) range 2 invert
true minimalBounds true modelId #7; wait 1; volume #7 level 0.5 step 1 color
#B2B2FF; wait 1; surface dust #7 size 40

> regen

> view frame1

> cofr

Center of rotation: 181.15 180.79 181.45 fixed  

> view position #7 sameAsModels #10

> wait 1

> set maxFrameRate 25

> windowsize 1080 1080

> view frame1

> movie record supersample 3

> wait 1

> coordset #10 1,181

> roll 0.133,0.0389,0.989 1.988950276243094 181 coordinateSystem #10 models #7
center 160,176,0

> wait 181

> wait 1

> movie stop

> movie encode test.mp4 quality high

Movie saved to test.mp4  
  

> regen

> view frame1

> view position #7 sameAsModels #10

> wait 1

> cofr

Center of rotation: 181.15 180.79 181.45 fixed  

> set maxFrameRate 25

> windowsize 1080 1080

> view frame1

> movie record supersample 3

> wait 1

> coordset #10 1,181

> roll 0.133,0.0389,0.989 1.988950276243094 181 coordinateSystem #10 models #7
center 160,176,0

> wait 181

> perframe "turn y -3.6" frames 50

> wait 50

> coordset #10 1,181

> roll 0.133,0.0389,0.989 1.988950276243094 181 coordinateSystem #10 models #7
center 160,176,0

> wait 181

> perframe "turn y -3.6" frames 50

> wait 50

> wait 1

> movie stop

> movie encode test_full2.mp4 quality high

Movie saved to test_full2.mp4  
  

> select up

16 atoms, 14 bonds, 1 model selected  

> select up

265 atoms, 274 bonds, 1 model selected  

> select up

5681 atoms, 5816 bonds, 1 model selected  

> hide sel atoms

> select #10/f:70@CZ

1 atom, 1 model selected  

> select up

11 atoms, 11 bonds, 1 model selected  

> select up

216 atoms, 221 bonds, 1 model selected  

> select up

496 atoms, 507 bonds, 1 model selected  

> hide sel atoms

> show #10 atoms

> select clear

> view frame1

> regen

> set maxFrameRate 25

> windowsize 1080 1080

> view frame1

> movie record supersample 3

> wait 1

> coordset #10 1,181

> roll 0.133,0.0389,0.989 1.988950276243094 181 coordinateSystem #10 models #7
center 160,176,0

> wait 181

> perframe "turn y -3.6" frames 50

> wait 50

> view position #7 sameAsModels #10

> wait 1

> coordset #10 1,181

> roll 0.133,0.0389,0.989 1.988950276243094 181 coordinateSystem #10 models #7
center 160,176,0

> wait 181

> perframe "turn y -3.6" frames 50

> wait 50

> wait 1

> movie stop

> movie encode test_full2.mp4 quality high

Movie saved to test_full2.mp4  
  

> coordset slider #10

> view position #7 sameAsModels #10

> wait 1

> set maxFrameRate 25

> windowsize 1080 1080

> view frame1

> movie record supersample 3

> wait 1

> coordset #10 1,181

Unknown command: roll0.17922030,0.02970853,0.98336030 129.12807513
coordinateSystem #10 models #7 center 146.73268993,176.43921115,0.00000000  

> wait 181

> perframe "turn y -3.6" frames 50

> wait 50

> view position #7 sameAsModels #10

> wait 1

> coordset #10 1,181

> roll 0.17922030,0.02970853,0.98336030 129.12807513 coordinateSystem #10
models #7 center 146.73268993,176.43921115,0.00000000

> wait 181

> perframe "turn y -3.6" frames 50

> wait 50

> wait 1

> movie stop

> movie encode test_full3.mp4 quality high

Movie saved to test_full3.mp4  
  

> stop

> regen

> view position #7 sameAsModels #10

> wait 1

> set maxFrameRate 25

> windowsize 1080 1080

> view frame1

> movie record supersample 3

> wait 1

> coordset #10 1,181

> roll 0.17922030,0.02970853,0.98336030 -1.988950276243094 181
coordinateSystem #10 models #7 center 146.73268993,176.43921115,0.00000000

> wait 181

> perframe "turn y -3.6" frames 50

> wait 50

> view position #7 sameAsModels #10

> wait 1

> coordset #10 1,181

> roll 0.17922030,0.02970853,0.98336030 -1.988950276243094 181
coordinateSystem #10 models #7 center 146.73268993,176.43921115,0.00000000

> wait 181

> perframe "turn y -3.6" frames 50

> wait 50

> wait 1

> movie stop

> movie encode test_full3.mp4 quality high

Movie saved to test_full3.mp4  
  

> view position #7 sameAsModels #10

> wait 1

> set maxFrameRate 25

> windowsize 1080 1080

> view frame1

> movie record supersample 3

> wait 1

> coordset #10 1,181

> roll 0.17922030,0.02970853,0.98336030 1.988950276243094 181 coordinateSystem
#10 models #7 center 146.73268993,176.43921115,0.00000000

> wait 181

> perframe "turn y -3.6" frames 50

> wait 50

> view position #7 sameAsModels #10

> wait 1

> coordset #10 1,181

> roll 0.17922030,0.02970853,0.98336030 1.988950276243094 181 coordinateSystem
#10 models #7 center 146.73268993,176.43921115,0.00000000

> wait 181

> perframe "turn y -3.6" frames 50

> wait 50

> wait 1

> movie stop

> movie encode test_full3.mp4 quality high

Movie saved to test_full3.mp4  
  

> regen

> view position #7 sameAsModels #10

> turn 0.10538144,-0.01332825,0.99434255 108.22343402 coordinateSystem #10
models #7 center 167.83361743,188.93439760,0.00000000

> move 0.10538144,-0.01332825,0.99434255 0.03427099 coordinateSystem #10
models #7

> turn 0.17922030,0.02970853,0.98336030 129.12807513 coordinateSystem #10
models #7 center 146.73268993,176.43921115,0.00000000

> move 0.17922030,0.02970853,0.98336030 -1.25194283 coordinateSystem #10
models #7

> turn 0.11417876,0.07470527,0.99064743 123.00295166 coordinateSystem #10
models #7 center 165.68116908,164.10104013,0.00000000

> move 0.11417876,0.07470527,0.99064743 1.16060753 coordinateSystem #10 models
#7

> regen

> hide #!7 models

> show #!1 models

> show #!2 models

> show #!3 models

> hide atoms

> show #10/s1 cartoons

> show #1/s1 cartoons

> show #2/s1 cartoons

> show #3/s1 cartoons

> hide #!10 models

> hide #!1 models

> show #!1 models

> show #1/s1 cartoons

> select #1/s1

337 atoms, 347 bonds, 1 model selected  

> show #1/s1 target abp

> hide #1/s1 target abp

> show #1/s1 target c

> hide #1/s1 target c

> show #1/s1 target abp

> show #1/s1 target abp

> hide #1/s1 target abp

> hide #1/s1 target c

> hide #1/s1 target c

> hide #!1 models

> show #!1 models

> hide #1 cartoons

> show #1/s1 cartoons

> select clear




OpenGL version: 3.3.0 NVIDIA 418.56
OpenGL renderer: GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (6)

comment:1 by Eric Pettersen, 6 years ago

Cc: Elaine Meng added
Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → hide/show confusing

in reply to:  2 ; comment:2 by Elaine Meng, 6 years ago 

We've already discussed this a lot.  See ticket #2272.

in reply to:  3 ; comment:3 by yazan.abbas@…, 6 years ago 

Hi,

I think I am reporting a different problem. Looking at my log. I was trying
to show the cartoon for #1/s1. I believe the following commands are all
from the GUI. I remember the command-line commands like show #1/s1 target c
or show #1/s c were also not working. I've encountered this issue several
times. I just have to keep randomly clicking on different models and
different views before the intended chain in the intended representation
appears.

 > show #1/s1 cartoons *Didn't show*
 > show #2/s1 cartoons *works*
 > show #3/s1 cartoons *works*
 > hide #!10 models
 > hide #!1 models
 > show #!1 models* #1/s1 still now showing*
 > show #1/s1 cartoons *still not showing*
 > select #1/s1 *test if selection works*
 337 atoms, 347 bonds, 1 model selected
 > show #1/s1 target abp *works*
 > hide #1/s1 target abp
 > show #1/s1 target c *still not showing*
 > hide #1/s1 target c
 > show #1/s1 target abp *this is still fine*
 > show #1/s1 target abp
 > hide #1/s1 target abp
 > hide #1/s1 target c
 > hide #1/s1 target c
 > hide #!1 models
 > show #!1 models
 > hide #1 cartoons
 > show #1/s1 cartoons* <-- Finally worked*
 > select clear

On Wed, Aug 14, 2019 at 2:12 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

in reply to:  4 ; comment:4 by Elaine Meng, 6 years ago 

The model has to be shown in order to enable any other kind of display.   This is the “S” checkbox in the Model Panel.  If you don’t have the model shown, you can’t show its atoms or ribbons.  The reason we have a model-shown level is that you can turn it on and off without affecting which individual atoms and per-residue ribbon segments are shown.

in reply to:  5 ; comment:5 by Elaine Meng, 6 years ago 

Pardon me, it's no longer an “S” but an eye icon in the Model Panel.  Also you can use commands like “show #1 models” “hide #1 models"

comment:6 by Tom Goddard, 6 years ago

Resolution: → can't reproduce
Status: assigned → closed

So a model is shown but "show #1/s1 cartoons" does not in some cases show the cartoon. That looks like a bug, but we would need a test case to figure it out. Showing cartoons is of course done a lot in ChimeraX and this has never been reported before, so some exceptional situation must be needed to produce this error.

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