# Avogadro quit unexpectedly **URL:** \ **Category:** Support\ **Created:** [August 31, 2022, 9:01pm UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953 "2022-08-31T21:01:04Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![teslim](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/teslim/32/1209_2.png) [@teslim](https://discuss.avogadro.cc/u/teslim)\ **Post date:** [August 31, 2022, 9:01pm UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953/1 "2022-08-31T21:01:04Z")
Hello admin, I have been running Avogadro on Mac for few months and this issue has been a great headache for me. This issue do arise when you try opening 2-3 PDBs (one at a time) or a big molecule with 780 atoms. Please attached image. Could it be that it’s just a MACOSx issue? ![image](https://discuss.avogadro.cc/uploads/default/original/2X/b/b18bc951771fc375a979e518a3767468aa537fc7.png) ---
**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:** [September 1, 2022, 12:46am UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953/2 "2022-09-01T00:46:30Z")
It’s hard to know more without the text of the report, which might indicate what exactly is crashing. Depending on what features you use, you might want to try a nightly build of Avogadro2: [https://two.avogadro.cc/](https://two.avogadro.cc/) which is what I use on my MacBook. I can definitely attest that it’ll read 2-3 PDBs or thousands of atoms without breaking a sweat. ---
**Author:** ![teslim](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/teslim/32/1209_2.png) [@teslim](https://discuss.avogadro.cc/u/teslim)\ **Post date:** [September 1, 2022, 1:05am UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953/3 "2022-09-01T01:05:33Z")
Thanks @ghutchis. I have tried opening the PDB (with 780 atoms) with Avogadro2 and was unsuccessful because the software closed immediately. I got the same result with Avogadro (1.20). Meanwhile, I tried opening the same PDB with two windows computer and was successful. Only the strong PC (with 16GB RAM) has all its Avogadro’s GUI functions working appropriately while the other has only it’s Zoom In/Out function active but the navigation tool (F9) button is unresponsive. ---
**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:** [September 1, 2022, 3:13am UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953/4 "2022-09-01T03:13:25Z")
Can you please send me the file or a link to the file? ---
**Author:** ![teslim](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/teslim/32/1209_2.png) [@teslim](https://discuss.avogadro.cc/u/teslim)\ **Post date:** [September 1, 2022, 2:16pm UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953/5 "2022-09-01T14:16:44Z")
Here it is [https://drive.google.com/file/d/1S8fxCYmSAgQMWchJFWfqGlry2naIScve/view?usp=sharing](https://drive.google.com/file/d/1S8fxCYmSAgQMWchJFWfqGlry2naIScve/view?usp=sharing) ---
**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:** [September 1, 2022, 3:40pm UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953/6 "2022-09-01T15:40:59Z")
Thanks! I’m curious what program created that PDB file. Avogadro should _ **never** _ crash, but it’s very much non-standard which is why there were problems. There’s a fix for Avo2 here: > > > Reported by teslim on the forum: > https://discuss.avogadro.cc/t/avogadro-quit-un…expectedly/3953/5 > > Signed-off-by: Geoff Hutchison \ > > 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. In about an 60-90 minutes there should be a link to a Mac build for you added as a comment on that GitHub link. ---
**Author:** ![teslim](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/teslim/32/1209_2.png) [@teslim](https://discuss.avogadro.cc/u/teslim)\ **Post date:** [September 1, 2022, 4:30pm UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953/7 "2022-09-01T16:30:14Z")
Thanks @ghutchis. The PDB was created with python using a monomeric unit (created in Avogadro). I will watch out for the fix. See attached error message for Avogadro 1.20 and Avogadro2. Thanks! [Avogadro 1.20 error report](https://drive.google.com/file/d/1QlHcTT9V9rVk4C_KZFOd3ZVp7yOuLi_a/view?usp=sharing) [Avogadro2 error report](https://drive.google.com/file/d/1GmjlaMw48TeEpEv99xxVoBU-RmR6d5px/view?usp=sharing) ---
**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:** [September 1, 2022, 4:44pm UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953/8 "2022-09-01T16:44:44Z")
If a Python program you wrote, I’d suggest a few minor tweaks for compatibility beyond Avogadro: - if it’s not a standard residue (amino acid, nucleic acid) you should use `HETATM` instead of `ATOM` - Make sure to add the element symbol in columns 77-78 (this was the cause of the crash): [wwPDB Format version 3.3: Coordinate Section](https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM) - Use integers for `CONECT` lines - right now some of these are ignored because they have values like `1.0` and `2.0` and C++ or Fortran codes won’t convert those to integers: [wwPDB Format version 3.3: Connectivity Section](https://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT) ---
**Author:** ![teslim](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/teslim/32/1209_2.png) [@teslim](https://discuss.avogadro.cc/u/teslim)\ **Post date:** [September 1, 2022, 5:49pm UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953/9 "2022-09-01T17:49:00Z")
Thanks @ghutchis. I will follow your advice. Super appreciate 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:** [September 2, 2022, 12:49am UTC](https://discuss.avogadro.cc/t/avogadro-quit-unexpectedly/3953/10 "2022-09-02T00:49:23Z")
The Mac build is here: [https://github.com/OpenChemistry/avogadrolibs/suites/8099621167/artifacts/349920174](https://github.com/OpenChemistry/avogadrolibs/suites/8099621167/artifacts/349920174) You should also be able to use a “nightly build” from [https://two.avogadro.cc/](https://two.avogadro.cc/) fairly soon since the fix has been merged into the main code.