# Crash when deleting atoms from pdb file **URL:** \ **Category:** Support\ **Created:** [January 6, 2026, 11:18pm UTC](https://discuss.avogadro.cc/t/crash-when-deleting-atoms-from-pdb-file/7270 "2026-01-06T23:18:55Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![myoung](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/m/ad7895/32.png) [@myoung](https://discuss.avogadro.cc/u/myoung)\ **Post date:** [January 6, 2026, 11:18pm UTC](https://discuss.avogadro.cc/t/crash-when-deleting-atoms-from-pdb-file/7270/1 "2026-01-06T23:18:55Z")
Avogadro2 locks up when I use the selection tool or the drawing tool to delete some atoms in a pdb file. I see that this was an (old) issue in Avogadro1 that was addressed. Indeed when I try this in Avogadro1 there is no problem using either tool to delete atoms from the same file. Bug? ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [January 7, 2026, 12:21am UTC](https://discuss.avogadro.cc/t/crash-when-deleting-atoms-from-pdb-file/7270/2 "2026-01-07T00:21:37Z")
It should never “lock up” - can you be a bit clearer? A screenshot or screencast? Thanks Having an example file would also help. ---
**Author:** ![myoung](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/m/ad7895/32.png) [@myoung](https://discuss.avogadro.cc/u/myoung)\ **Post date:** [January 7, 2026, 12:56am UTC](https://discuss.avogadro.cc/t/crash-when-deleting-atoms-from-pdb-file/7270/3 "2026-01-07T00:56:52Z")
Sorry I wasn’t more clear. Avogadro2 simply stopped responding as evidenced by the spinning cursor and the status in Activity Monitor. This was with either the current version or the nightly build (from a week or two ago). This is on MacOS Sequoia fully up to date. Example pdb file attached. Thanks for your time. [example.pdb](https://discuss.avogadro.cc/uploads/short-url/g9idwsqAky9a6r5EamP5QAOyIq7.pdb) (8.8 KB) ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [January 7, 2026, 1:09am UTC](https://discuss.avogadro.cc/t/crash-when-deleting-atoms-from-pdb-file/7270/4 "2026-01-07T01:09:49Z")
Okay, I’ll give it a look. If it stopped responding on the Mac, that’s pretty easy for me to debug if I can reproduce it ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [January 16, 2026, 2:50pm UTC](https://discuss.avogadro.cc/t/crash-when-deleting-atoms-from-pdb-file/7270/5 "2026-01-16T14:50:30Z")
This set of patches should do it. I fixed the PDB example, then found another bug when trying to delete atoms from ORCA files. (Seems unlikely, but finally found the underlying bug.) > > > Bonds were added but with the same unique id > > Developer Certificate of Origin > … > Version 1.1 > > Copyright (C) 2004, 2006 The Linux Foundation and its contributors. > 1 Letterman Drive > Suite D4700 > San Francisco, CA, 94129 > > Everyone is permitted to copy and distribute verbatim copies of this > license document, but changing it is not allowed. > > > Developer's Certificate of Origin 1.1 > > By making a contribution to this project, I certify that: > > (a) The contribution was created in whole or in part by me and I > have the right to submit it under the open source license > indicated in the file; or > > (b) The contribution is based upon previous work that, to the best > of my knowledge, is covered under an appropriate open source > license and I have the right under that license to submit that > work with modifications, whether created in whole or in part > by me, under the same open source license (unless I am > permitted to submit under a different license), as indicated > in the file; or > > (c) The contribution was provided directly to me by some other > person who certified (a), (b) or (c) and I have not modified > it. > > (d) I understand and agree that this project and the contribution > are public and that a record of the contribution (including all > personal information I submit with it, including my sign-off) is > maintained indefinitely and may be redistributed consistent with > this project or the open source license(s) involved. > > > > \## Summary by CodeRabbit > > \* \*\*Refactor\*\* > \* Improved internal atom and bond identifier management systems for enhanced consistency. > \* Optimized method dispatch mechanisms for atom operations. > > \✏️ Tip: You can customize this high-level summary in your review settings.\ ---
**Author:** ![myoung](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/m/ad7895/32.png) [@myoung](https://discuss.avogadro.cc/u/myoung)\ **Post date:** [January 17, 2026, 5:35am UTC](https://discuss.avogadro.cc/t/crash-when-deleting-atoms-from-pdb-file/7270/6 "2026-01-17T05:35:49Z")
Awesome. Thanks for addressing this.