Can not open classes_00.hdf

[Reeham Victor]

Hi,

I hope you’re doing well.

I’m working on a reconstruction for a class project following the Blake protocol. When I reach step 9, where I need to select good classes, I double-click on r2db_01 and then classes_00.hdf. However, instead of opening a new window, I only see a small watch icon, and nothing loads.

I’m not sure what’s causing this issue and would really appreciate any guidance you could provide.

Thank you for your time and help!

[Ludtke, Steven J.]

Sorry you're having issues. 

Take a look in the terminal window where you launched the project manager from. There is likely some sort of error message which might help us sort out what's going on. 

Looks like you're running on a Mac?   Posting the full output of the e2version.py command would also be helpful.

cheers

---

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

On Sep 18, 2025, at 6:46 PM, Reeham Victor <reeham...@gmail.com> wrote:

Hi,

I hope you’re doing well.

I’m working on a reconstruction for a class project following the Blake protocol. When I reach step 9, where I need to select good classes, I double-click on r2db_01 and then classes_00.hdf. However, instead of opening a new window, I only see a small watch icon, and nothing loads.

I’m not sure what’s causing this issue and would really appreciate any guidance you could provide.

<processed-7B771987-82D2-438A-9E2C-FD48CF649D71.jpeg>

Thank you for your time and help!

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<processed-7B771987-82D2-438A-9E2C-FD48CF649D71.jpeg>

[Reeham Victor]

Thank you for such a quick response. It is a mac. Here's what my terminal says:

Last login: Thu Sep 18 19:56:30 on ttys000

(base) reehamvictor@Reehams-MacBook-Air ~ % cd /Users/reehamvictor/miniforge3/envs/eman2/lib/python3.10/site-packages/eman2_gui/

ls *.pyc

zsh: no matches found: *.pyc

(base) reehamvictor@Reehams-MacBook-Air eman2_gui % conda deactivate

conda activate eman2

cd ~/Desktop/workshop_2016

(eman2) reehamvictor@Reehams-MacBook-Air workshop_2016 % e2projectmanager.py &

[1] 2497

(eman2) reehamvictor@Reehams-MacBook-Air workshop_2016 % qt.qpa.fonts: Populating font family aliases took 108 ms. Replace uses of missing font family ".AppleSystemUIFont" with one that exists to avoid this cost. 

Traceback (most recent call last):

  File "/Users/reehamvictor/miniforge3/envs/eman2/lib/python3.10/site-packages/eman2_gui/embrowser.py", line 484, in show2dStack

    target = brws.view2ds[-1]

IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

  File "/Users/reehamvictor/miniforge3/envs/eman2/lib/python3.10/site-packages/eman2_gui/embrowser.py", line 4112, in buttonMisc

    try: self.curactions[num][2](self) # This calls the action method

  File "/Users/reehamvictor/miniforge3/envs/eman2/lib/python3.10/site-packages/eman2_gui/embrowser.py", line 492, in show2dStack

    target.set_data(self.path, self.path)

  File "/Users/reehamvictor/miniforge3/envs/eman2/lib/python3.10/site-packages/eman2_gui/emimagemx.py", line 893, in set_data

    self.resize(min(x,mx),min(y,my))

  File "/Users/reehamvictor/miniforge3/envs/eman2/lib/python3.10/site-packages/eman2_gui/emapplication.py", line 110, in resize

    QtOpenGL.QGLWidget.resize(self, w, h)

TypeError: arguments did not match any overloaded call:

  resize(self, a0: QSize): argument 2 has unexpected type 'float'

  resize(self, w: int, h: int): argument 2 has unexpectedwhich e2projectmanager.pyich e2projectmanager.py

/Users/reehamvictor/miniforge3/envs/eman2/bin/e2projectmanager.py

(eman2) reehamvictor@Reehams-MacBook-Air workshop_2016 % grep -R "QGLWidget.resize" /Users/reehamvictor/miniforge3/envs/eman2/lib/python3.10/site-packages/eman2_gui/

To view this discussion visit https://groups.google.com/d/msgid/eman2/4E474FD4-0175-4291-BCC8-CB0CFF643771%40bcm.edu.

[Steve Ludtke]

It looks like you may be running an older version of EMAN2 with a newer version of PyQt (installed via conda/mamba). This looks like a bug we fixed quite a long time ago due to changes in the PyQt toolkit used for the GUI. 

If you post the output of "e2version.py",  and "conda list|grep -i qt" that would help confirm.  While it might be tempting to use an older version of EMAN2 when trying to run an older tutorial, we frequently make updates for compatibility with newer versions of MacOS, Qt and other toolkits, so running older versions may not always be readily possible.

To view this discussion visit https://groups.google.com/d/msgid/eman2/CABhWkXjN9y0ZxwrHGdqKnmnL6SYT6wJPTFVrvPABDD0z6Nx6yg%40mail.gmail.com.

[Reeham Victor]

This was the version I could find online. Is it possible to share the link to the new version?

e2version.py

EMAN 2.99.54 ( GITHUB: 2023-11-06 16:28 - commit: NOT-INSTALLED-FROM-GIT-REPO )

Your EMAN2 is running on: Mac OS 14.4.1 x86_64

Your Python version is: 3.10.13

(eman2) reehamvictor@Reehams-MacBook-Air ~ % conda list|grep -i qt

pyqt                      5.15.9          py310hecc045f_5    conda-forge

pyqt5-sip                 12.12.2         py310h018f80b_5    conda-forge

qt-main                   5.15.8              heb9da5c_15    conda-forge

(eman2) reehamvictor@Reehams-MacBook-Air ~ % 

To view this discussion visit https://groups.google.com/d/msgid/eman2/37D561B0-B75B-42D3-A03C-D02E541E7599%40gmail.com.

[Steve Ludtke]

Indeed, we haven't generated that style of binary for some time now. We've switched to a fully conda-based approach. Please follow the installation instructions at:

To view this discussion visit https://groups.google.com/d/msgid/eman2/CABhWkXg61kmQV4YBCkiMMYbm%3D8hJksSHioUTkhJ0dXw0pRKMRQ%40mail.gmail.com.

[Reeham Victor]

Okay, I was able to get it working with the new version. 

e2version.py

EMAN 2.99.70 ( GITHUB: 2025-06-25 02:27 - commit: NOT-INSTALLED-FROM-GIT-REPO )

Your EMAN2 is running on: Mac OS 14.4.1 arm64

Your Python version is: 3.12.11

(eman2) reehamvictor@Reehams-MacBook-Air workshop_2016 % 

Thank you so much for your support.

To view this discussion visit https://groups.google.com/d/msgid/eman2/D0F02DAE-0E37-46A8-A1BD-1D7132DB6756%40gmail.com.