Add-ons: Import-Export: Atomic Blender PDB/XYZ division error #105322
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Reference: blender/blender-addons#105322
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System Information
Operating system: Windows-10-10.0.22631-SP0 64 Bits
Graphics card: NVIDIA GeForce RTX 4060/PCIe/SSE2 NVIDIA Corporation 4.6.0 NVIDIA 552.22
Blender Version
Broken: version: version: 4.0.2, branch: blender-v4.0-release, commit date: 2023-12-05 07:41, hash:
9be62e85b727
Worked: (newest version of Blender that worked as expected)
Addon Information
Name: Atomic Blender PDB/XYZ (1, 8, 1)
Author: Clemens Barth
Short description of error
Dear developer.
When I imported the attached file 'Cabon monooxide_v1.pdb with the addon, it showed error massage below.
Then, I found by chance that slight differenct coordinations with same structure works without error: the attached 'Carbon monooxide_v2.pdb' file. Whether I turn on the 'bonds' option or not.
In another case, the attached 'acetonitirile3_cd_ob.pdb' file only works without checking 'bonds' in import option (the option for double and triple bonds). with enabling the option, it resulting the following error:
I have failed to figure out the solution in my ability. Please check this issue.
Many thanks,
Sincerely yours,
Exact steps for others to reproduce the error
The error have been reproduced with newely installed blender 4.0 and 4.1 either. and distinct PCs. newely installed blender opened, check addon 'atomic blender PDB/XYZ' in preference, file-import-PDB, then import the attached file with default options.
Hi, thanks for the report. Can confirm
@Blendphys 👋
Dear @Byeongyoon-Kim and @PratikPB2123.
I confirm this error. It seems that the bonds should not be in the XY plane (and other planes also?) ... so, as an emergency solution, just turn the molecule a little bit in the PDB file.
I will deal with this in the next days. Please, be patient: I have to re-build Blender from scratch ... ;-).
Cheers.
No problem, thanks for checking :)
Dear @Byeongyoon-Kim and @PratikPB2123.
I have finished my work, it should run now without any issues.
Note that I could not upload the new version because of a current philosophy change of all Blender add-ons (see here: https://devtalk.blender.org/t/changes-to-add-on-bundling-4-2-onwards/34593) - the repository is read-only so far.
For the newest version of Blender currently under construction (Blender 4.2 and onwards) , I have started to update the add-on in its new repository: https://projects.blender.org/extensions/io_mesh_atomic. There you can see also my commit I have done today.
Fast fix: for all those of you, who work with the current or an older version, just replace 'pdb_import.py' with the new version attached to this message (see below).
Let me know if things work, thx.
@PratikPB2123 , if I forget to close this report, just do it for me ... thx. ;-)
Thanks. For some reason I'm not able to activate add-on after installing it from extensions platforms :/
Will close as the fix has already been pushed to repo:
1a938c45f1
Wonderful! You are my hero! Thanks for your commitment.
The replaced pdb_import.py works perfectly 🎉
I also will happily wait for the new Blender 4.2 to be released.