Problem reshowing volume series

[sitins07@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-42-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.9 (2019-01-12)
Description
While several (5) volume series opened, also the corresponding bars are created, when you press hide in volume viewer on one of the series and move the bar (occasionaly) you cannot make visible the whole series again (tryed: press show in volume viewer, pressed show in checkbox in model panel on each volume in seriaes and the top one, tryed to move the series bar to animate, commands show #5 and show #5.4 (no error and no result)) 


Log:
> toolshed show "Density Map Toolbar"

UCSF ChimeraX version: 0.9 (2019-01-12)  
How to cite UCSF ChimeraX  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder_try2_less-
translation/analyse_component001_bin0??.mrc vseries true

Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder_try2_less-
translation/analyse_component002_bin0??.mrc vseries true

Opened map series analyse_component002_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0846, step 1, values float32  

> vseries slider #2

> vseries slider #1

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder_try2_less-
translation/analyse_component003_bin0??.mrc vseries true

Opened map series analyse_component003_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0846, step 1, values float32  

> vseries slider #3

> vseries slider #2

> close #1 #2 #3

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try1/analyse_component001_bin0??.mrc vseries true

File not found:
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try1/analyse_component001_bin0??.mrc  

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try1/analyse_component001_bin0??.mrc vseries true

Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32  

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try1/analyse_component002_bin0??.mrc vseries true

Opened map series analyse_component002_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0849, step 1, values float32  

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try1/analyse_component003_bin0??.mrc vseries true

Opened map series analyse_component003_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32  

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try1/analyse_component004_bin0??.mrc vseries true

Opened map series analyse_component004_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0851, step 1, values float32  

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try1/analyse_component005_bin0??.mrc vseries true

Opened map series analyse_component005_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32  

> vseries slider #1

> vseries slider #2

> vseries slider #3

> vseries slider #4

> vseries slider #5

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting simple

> open /home/vpetryc/Projects/nch/MultiBody/nc_272_focustc15A_10_5A_c3.mrc

Opened nc_272_focustc15A_10_5A_c3.mrc, grid size 272,272,272, pixel 1.16,
shown at level 0.04, step 2, values float32  

> open /home/vpetryc/Projects/nch/MultiBody/nc_272_focustc15A_10_5A_c4.mrc

Opened nc_272_focustc15A_10_5A_c4.mrc, grid size 272,272,272, pixel 1.16,
shown at level 0.0404, step 2, values float32  

> open /home/vpetryc/Projects/nch/MultiBody/nc_272_focustc15A_10_5A_c5.mrc

Opened nc_272_focustc15A_10_5A_c5.mrc, grid size 272,272,272, pixel 1.16,
shown at level 0.0423, step 2, values float32  

> open /home/vpetryc/Projects/nch/MultiBody/nc_272_focustc15A_10_5A_c7.mrc

Opened nc_272_focustc15A_10_5A_c7.mrc, grid size 272,272,272, pixel 1.16,
shown at level 0.0421, step 2, values float32  

> open /home/vpetryc/Projects/nch/MultiBody/nc_272_focustc15A_10_5A_c9.mrc

Opened nc_272_focustc15A_10_5A_c9.mrc, grid size 272,272,272, pixel 1.16,
shown at level 0.0425, step 2, values float32  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> fitmap #7 inMap #1.1

Fit map nc_272_focustc15A_10_5A_c4.mrc in map analyse_component001_bin001.mrc
using 218466 points  
correlation = 0.9515, correlation about mean = 0.6855, overlap = 319  
steps = 72, shift = 16.3, angle = 2.01 degrees  
  
Position of nc_272_focustc15A_10_5A_c4.mrc (#7) relative to
analyse_component001_bin001.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.99995921 0.00219292 -0.00876129 -7.50359201  
-0.00189548 0.99942634 0.03381417 -15.43997082  
0.00883042 -0.03379619 0.99938973 -5.27926179  
Axis -0.96612415 -0.25137832 -0.05842152  
Axis point 0.00000000 -143.10042773 369.14516562  
Rotation angle (degrees) 2.00521808  
Shift along axis 11.43909791  
  

> fitmap #10 inMap #1.1

Fit map nc_272_focustc15A_10_5A_c9.mrc in map analyse_component001_bin001.mrc
using 155718 points  
correlation = 0.963, correlation about mean = 0.6286, overlap = 300.4  
steps = 72, shift = 16.1, angle = 2.58 degrees  
  
Position of nc_272_focustc15A_10_5A_c9.mrc (#10) relative to
analyse_component001_bin001.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.99989321 -0.00665499 -0.01301076 -5.10385606  
0.00720362 0.99906684 0.04258578 -18.15967105  
0.01271521 -0.04267496 0.99900809 -4.42871403  
Axis -0.94598307 -0.28543425 0.15376382  
Axis point 0.00000000 -145.78086037 360.69240375  
Rotation angle (degrees) 2.58288747  
Shift along axis 9.33057760  
  

> show #!1 models

> vseries slider #1

> close #1

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try1/analyse_component001_bin0??.mrc vseries true

Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32  

> vseries slider #1

> fitmap #9 inMap #1.1

Fit map nc_272_focustc15A_10_5A_c7.mrc in map analyse_component001_bin001.mrc
using 173821 points  
correlation = 0.9572, correlation about mean = 0.632, overlap = 307.4  
steps = 68, shift = 16.3, angle = 2.1 degrees  
  
Position of nc_272_focustc15A_10_5A_c7.mrc (#9) relative to
analyse_component001_bin001.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.99993117 0.00280089 -0.01139386 -7.12762886  
-0.00240350 0.99939339 0.03474311 -15.38011241  
0.01148426 -0.03471334 0.99933132 -5.59323082  
Axis -0.94740521 -0.31206392 -0.07098932  
Axis point 0.00000000 -143.10125947 332.85249817  
Rotation angle (degrees) 2.10071307  
Shift along axis 11.94939048  
  

> close session

> select up

Nothing selected  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_1/analyse_component001_bin0??.mrc
vseries true

Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0851, step 1, values float32  

> close #1

> open /home/vpetryc/cluster/projects/Tu/nch/Refine3D/128_nch_tc_shoulder-
tc_comp1_-11_-6/run_class001.mrc

Opened run_class001.mrc, grid size 128,128,128, pixel 2.32, shown at level
0.0653, step 1, values float32  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder_try2_less-
translation/analyse_component001_bin0??.mrc vseries true

Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder_try2_less-
translation/analyse_component001_bin0??.mrc vseries true

Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32  

> open /home/vpetryc/cluster/projects/Tu/nch/Refine3D/128_nch_tc_shoulder-
tc_comp1_5_10/run_it008_half2_class001.mrc

Opened run_it008_half2_class001.mrc, grid size 128,128,128, pixel 2.32, shown
at level 0.0521, step 1, values float32  

> close #1

> close #2

> close #3

> close #4

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try2-fixed_body/analyse_component001_bin0??.mrc vseries true

Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0841, step 1, values float32  

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try2-fixed_body/analyse_component002_bin0??.mrc vseries true

Opened map series analyse_component002_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0844, step 1, values float32  

> show #!2.9 models

> hide #!2 models

> show #!2.1 models

> hide #!2.10 models

> show #!2.10 models

> vseries slider #1

> vseries slider #2

> show #!2.10 models

> hide #!2.8 models

> hide #!2 models

> show #!2 models

> close #2

> hide #!1.10 models

> close #1

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try2-fixed_body/analyse_component001_bin0??.mrc vseries true

Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0841, step 1, values float32  

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try2-fixed_body/analyse_component002_bin0??.mrc vseries true

Opened map series analyse_component002_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0844, step 1, values float32  

> vseries slider #1

> vseries slider #2

> open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder-
tc_try2-fixed_body/analyse_component003_bin0??.mrc vseries true

Opened map series analyse_component003_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0841, step 1, values float32  

> vseries slider #3

> close #1

> close #2

> close #3

> select up

Nothing selected  

> select up

Nothing selected  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component001_bin0??.mrc
vseries true

File not found:
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component001_bin0??.mrc  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component001_bin0??.mrc
vseries true

Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0846, step 1, values float32  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component002_bin0??.mrc
vseries true

Opened map series analyse_component002_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0851, step 1, values float32  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component003_bin0??.mrc
vseries true

Opened map series analyse_component003_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0849, step 1, values float32  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component004_bin0??.mrc
vseries true

Opened map series analyse_component004_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0853, step 1, values float32  

> open
/home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component005_bin0??.mrc
vseries true

Opened map series analyse_component005_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0868, step 1, values float32  

> vseries slider #1

> vseries slider #2

> vseries slider #3

> vseries slider #4

> vseries slider #5

> show #!5.1 models

> hide #!5.2 models

> show #!5.2 models

> hide #!5 models

> show #!5 models

> show #!5.3 models

> show #!5.4 models

> show #!5.10 models

> show #!5.9 models

> show #!5.8 models

> show #!5.7 models

> show #!5.6 models

> hide #!5 models

> show #!5 models

> show #5

> show #5

> show #5.4




OpenGL version: 3.3.0 NVIDIA 390.87
OpenGL renderer: Quadro 2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

Can you produce this problem in a simple way? I tried and was not able to reproduce the problem.

But I have a hunch about why the volume series is not shown. There may be no threshold set. Does the volume viewer panel show a vertical bar on the histogram for the invisible series? If there is no vertical bar then there is no threshold set and no surface will appear. I'm not sure how that can happen. You can ctrl-click or right click on the histogram to show a menu and choose "New Threshold" to add a surface threshold level. Maybe this is not the problem -- I just tried deleting the threshold (using the menu) and then moved the volume series slider and it created a new threshold level. If you use the histogram menu and choose "Show outline box" for the invisible series does it show an outline?

[sitins07@…]

You are absolutely right, I moved threshold, and adding a new one on the
histogram solves the problem. Thank you.

Respectfully yours,
Valentyn Petrychenko


вт, 15 січ. 2019 о 20:58 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> пише:

[Tom Goddard]

Not sure how you removed the threshold. Perhaps there is a bug where the volume series slider removes it. If you see it again and figure out the steps that leave you with no threshold level, report another bug (menu Help / Report a Bug...), because I'd like to fix it.