Cannot change level of flipped map

[andrew.alexander@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
After using the command "volume flip #1" I can not change the level of the newly generated map. Thanks

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/andrew/Library/CloudStorage/OneDrive-
> ETHZurich/DATA/PROCESSING/ScALG3_processing/ScALG3-D71N-Fab16-Nb-ternary-
> dataset-1-2023.07.14/J234/cryosparc_P50_J234_008_volume_map.mrc

Opened cryosparc_P50_J234_008_volume_map.mrc as #1, grid size 432,432,432,
pixel 0.648, shown at level 0.0124, step 2, values float32  

> volume flip #1

Opened cryosparc_P50_J234_008_volume_map.mrc z flip as #2, grid size
432,432,432, pixel 0.648, shown at step 1, values float32  

> volume #2 level 0.2

> volume #2 level 0.4

> volume #2 level 0

> volume #2 level 0.03




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac21,1
      Model Number: Z12R0009KSM/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 2 days, 2 hours, 44 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
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    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
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    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
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    ChimeraX-VTK: 1.0
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    colorama: 0.4.6
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[Tom Goddard]

It is working fine for me in ChimeraX 1.7 on Mac ARM. Maybe you had both the original and flipped map shown and the original one was at lower threshold and hid the flipped one.

I tried

open 1080 from emdb
volume flip #1
volume #2 level 0.5

[andrew.alexander@…]

Hello,

Thank for looking into this. It also works for me when I follow the steps you took to recreate this bug. However, I still have this issue when using maps processed in cryoSPARC that are a larger box size and therefore automatically load into ChimeraX with the step size set to 2. Z-flipping works if I set the step size to 1 for each map before flipping; however, if I don’t reset the step size then I am not able to adjust the contour of the resulting flipped map. Here is an example map if you want to reproduce this issue: ​https://urldefense.proofpoint.com/v2/url?u=https-3A__polybox.ethz.ch_index.php_s_XtB7Tfms1FnbLln&d=DwIGaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=CKzZmwKi9_YVvHng-0ezdJFE-0MROfpdFWLsI4CZgtQ&m=ba6AVo8sAvSOgryWiMJ3hP9WUcPTvIT72ksWCSvkkwOu6nYXh1VG-7pPmgUaTjU4&s=duWp2OOPgmlwDxp17FeE6CEn24kVM5_u94bYSglmB5o&e=

Cheers,
Andrew

---

Dr. J. Andrew N. Alexander
Postdoctoral fellow | Locher Lab
ETH Zürich
Institute of Molecular Biology and Biophysics
Otto-Stern-Weg 5, HPK G4
8093 Zürich, Switzerland
andrew.alexander@…
Mobile: +41 76 232 36 53

---

[Tom Goddard]

Thanks for the tip about the step 2 being important. I tried with EMDB 28896 which opens at step 2 and the level changes on the flipped map. But when I tried with your cryosparc map it does not change. I'll be able to figure this out and fix it with a bit more digging.

[andrew.alexander@…]

Great! Thanks a lot! Sorry I didn\u2019t give all the details up front; I actually only discovered them myself last weekend. 

Cheers,
Andrew
-----------------------------------------------------------------------
Dr. J. Andrew N. Alexander
Postdoctoral fellow | Locher Lab
ETH Zürich
Institute of Molecular Biology and Biophysics
Otto-Stern-Weg 5,  HPK G4                    
8093 Zürich, Switzerland   
andrew.alexander@mol.biol.ethz.ch 
Mobile: +41 76 232 36 53
-----------------------------------------------------------------------

[Tom Goddard]

Fixed.

This was convoluted error where the flipped volume did not properly cache the data it had read. The problem was not caused by "step 2". In fact it was that the unflipped map was big enough that its data was not kept in cache and the flipped volume did not restore its cached data.