Impossible to add missing atoms

[Mohamed-dev0]

Hi,

Every time I run fixer.addMissingAtoms(), my jupyter notbook crashes with

"Kernel Restarting The kernel for Untitled3.ipynb appears to have died. It will restart automatically"

Here is what I did before:

fixer.findMissingResidues()
fixer.missingResidues
fixer.findNonstandardResidues()
print(fixer.nonstandardResidues)
fixer.replaceNonstandardResidues()
fixer.removeHeterogens(keepWater=False)

Thank you for help,

Mohamed

[peastman]

First a few questions that will help understand how to debug it.

1. Describe your computer (OS, processor architecture, GPU model).
2. What is the output of conda list?
3. What is the output of python -m openmm.testInstallation?

[Mohamed-dev0]

1. Describe your computer (OS, processor architecture, GPU model). Operating System (OS): Windows 10 Pro Processor Architecture: x64 CPU Model: Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz Intel(R) HD Graphics 620 I dont have GPU model in my computer 1. What is the output of conda list? I have many packages from _openmp_mutex to zstd. 1. What is the output of python -m openmm.testInstallation? I have this on gitbash: C:\Users\PC\miniconda3\python.exe: No module named openmm.testInstallation? (base) And nothing on Jupyter lab when I run !python -m openmm.testInstallation De : Peter Eastman ***@***.***> Envoyé : samedi 8 novembre 2025 18:45 À : openmm/pdbfixer ***@***.***> Cc : Mohamed-dev0 ***@***.***>; Author ***@***.***> Objet : Re: [openmm/pdbfixer] Impossible to add missing atoms (Issue #341) [https://avatars.githubusercontent.com/u/4379786?s=20&v=4]peastman left a comment (openmm/pdbfixer#341)<#341 (comment)> First a few questions that will help understand how to debug it. 1. Describe your computer (OS, processor architecture, GPU model). 2. What is the output of conda list? 3. What is the output of python -m openmm.testInstallation? — Reply to this email directly, view it on GitHub<#341 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BNZDHHZUAWT23HVYED25Q2L33YTYJAVCNFSM6AAAAACLRDKOXCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKMBWG42DQNBZG4>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[peastman]

I have many packages from _openmp_mutex to zstd.

Again, please post the output.

C:\Users\PC\miniconda3\python.exe: No module named openmm.testInstallation?

That means you haven't installed OpenMM. Also, you're running in the base environment, which isn't a good idea. It's better to create a new environment:

conda create --name openmm openmm
conda activate openmm
python -m openmm.testInstallation