Scrollable Segger segment saving?

[posert@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
With ChimeraX fullscreened in Windows 10, saving all segments from a segger job to an .mrc file increases the window size beyond the maximum vertical resolution, pushing the bottom of the window out of view. Resizing and re-maximizing the window resolves the issue. This issue also occurred in ChimeraX 1.3. I believe it also happens when performing some other map iterations, but it always happens when saving a segment job to .mrc file.

Log:
> set bgColor white

UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\posert\\\Downloads\\\cryosparc_P36_J35_005_volume_map.mrc

Opened cryosparc_P36_J35_005_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.23, shown at level 0.039, step 1, values float32  

> volume #1 level 0.08359

> volume #1 level 0.08974

> volume gaussian #1 sDev 2

Opened cryosparc_P36_J35_005_volume_map.mrc gaussian as #2, grid size
256,256,256, pixel 1.23, shown at step 1, values float32  

> volume #2 level 0.05085

> ui tool show "Segment Map"

Segmenting cryosparc_P36_J35_005_volume_map.mrc gaussian, density threshold
0.050846  
Showing 25 region surfaces  
383 watershed regions, grouped to 25 regions  
Showing cryosparc_P36_J35_005_volume_map gaussian.seg - 25 regions, 25
surfaces  
Drag select of 568, 569, 4770 of 14624 triangles, 556, 4515 of 12156
triangles, 2 cryosparc_P36_J35_005_volume_map.mrc gaussian  
Deleted 3 regions  
Drag select of 561, 2306 of 35012 triangles, 564, 1246 of 29624 triangles,
563, 1411 of 20448 triangles, 558, 533, 565, 14162 of 14292 triangles, 562,
535, 889 of 10972 triangles, 534, 10062 of 10288 triangles, 536, 92 of 7804
triangles, 571, 546, 5965 of 6208 triangles, 2
cryosparc_P36_J35_005_volume_map.mrc gaussian  

> select clear

Drag select of 558, 533, 565, 7347 of 14292 triangles, 562, 12054 of 13528
triangles, 534, 6120 of 10288 triangles, 571, 7040 of 7100 triangles, 546,
3100 of 6208 triangles, 2 cryosparc_P36_J35_005_volume_map.mrc gaussian  
Deleted 7 regions  

> hide #!2 models

Saving 15 regions to mrc file...  
Opened cryosparc_P36_J35_005_volume_map_15_regions.mrc as #4, grid size
80,80,70, pixel 1.23, shown at step 1, values float32  
Wrote cryosparc_P36_J35_005_volume_map_15_regions.mrc  




OpenGL version: 3.3.0 NVIDIA 451.67
OpenGL renderer: Quadro P620/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision 3551
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 16,791,748,608
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
OSLanguage: en-US

Installed Packages:
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    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
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    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
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    ChimeraX-gltf: 1.0
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[Eric Pettersen]

Reported by Rich Posert

[Tom Goddard]

Can you send a screen capture showing the too tall ChimeraX?

Maybe what you see is that when you use Segment Map menu File / Save All Regions to .mrc File that a new histogram is shown in the Volume Viewer pane increasing its height which then makes the whole ChimeraX window too tall. I don't see that on Mac. I am wondering what it looks like -- what are all the tool panels you have on the right side of the ChimeraX window.

Did you know you can drag and stack the Tool panels on top of each other and then switch between them using the tabs at the bottom of the stacked panels? In general there simply isn't room to have lots of Tool panels arranged vertically at the right side of the ChimeraX window because they need too much vertical space.

[posert@…]

Hello, I did know that I could do that but hadn't tried it --- having all the panels in a single tabbed/stacked panel prevents this issue from occurring when saving the .mrc! So you're probably right that it's the addition of a new histogram.



I've attached a screenshot of my normal layout with the window size bug as well.



Thank you!



-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, August 9, 2022 12:49 PM
Cc: goddard@cgl.ucsf.edu; pett@cgl.ucsf.edu; Rich Posert <posert@ohsu.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #7420: Scrollable Segger segment saving?



#7420: Scrollable Segger segment saving?

-----------------------------------+-------------------------

          Reporter:  posert@…      |      Owner:  Tom Goddard

              Type:  defect        |     Status:  assigned

          Priority:  normal        |  Milestone:

         Component:  Input/Output  |    Version:

        Resolution:                |   Keywords:

        Blocked By:                |   Blocking:

Notify when closed:                |   Platform:  all

           Project:  ChimeraX      |

-----------------------------------+-------------------------

Changes (by Tom Goddard):



* cc: pett (added)





Comment:



Can you send a screen capture showing the too tall ChimeraX?



Maybe what you see is that when you use Segment Map menu File / Save All  Regions to .mrc File that a new histogram is shown in the Volume Viewer  pane increasing its height which then makes the whole ChimeraX window too  tall.  I don't see that on Mac.  I am wondering what it looks like -- what  are all the tool panels you have on the right side of the ChimeraX window.



Did you know you can drag and stack the Tool panels on top of each other  and then switch between them using the tabs at the bottom of the stacked  panels?  In general there simply isn't room to have lots of Tool panels  arranged vertically at the right side of the ChimeraX window because they  need too much vertical space.



--

Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7420*comment:2__;Iw!!Mi0JBg!Men2ihJsqtHwEwEnKb_3KsX6fbt3FdFKu2ZvhnCSTz8icLJzmuxPk9EX_s-agCyVl9BzCLaVCKqqoTYXtqb4wa4ZIVWuLRM$  <https://urldefense.com/v3/__https:/www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7420*comment:2__;Iw!!Mi0JBg!Men2ihJsqtHwEwEnKb_3KsX6fbt3FdFKu2ZvhnCSTz8icLJzmuxPk9EX_s-agCyVl9BzCLaVCKqqoTYXtqb4wa4ZIVWuLRM$%20%20> > ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!Mi0JBg!Men2ihJsqtHwEwEnKb_3KsX6fbt3FdFKu2ZvhnCSTz8icLJzmuxPk9EX_s-agCyVl9BzCLaVCKqqoTYXtqb4wa4Z1OwwkX8$  <https://urldefense.com/v3/__https:/www.rbvi.ucsf.edu/chimerax/__;!!Mi0JBg!Men2ihJsqtHwEwEnKb_3KsX6fbt3FdFKu2ZvhnCSTz8icLJzmuxPk9EX_s-agCyVl9BzCLaVCKqqoTYXtqb4wa4Z1OwwkX8$%20%20> > ChimeraX Issue Tracker

Screenshot 2022-08-10 100217.png​

[posert@…]

Added by email2trac

[Tom Goddard]

Glad stacking the panels works.

I think the window resizes too tall when the histogram of the new masked map is shown in the Volume Viewer panel. Possibly I can do something about that to make it not resize the main window. I will look into it.