Avogadro quit unexpectedly

teslim · August 31, 2022, 9:01pm

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?

ghutchis · September 1, 2022, 12:46am

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/ 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.

teslim · September 1, 2022, 1:05am

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.

ghutchis · September 1, 2022, 3:13am

Can you please send me the file or a link to the file?

teslim · September 1, 2022, 2:16pm

Here it is

https://drive.google.com/file/d/1S8fxCYmSAgQMWchJFWfqGlry2naIScve/view?usp=sharing

ghutchis · September 1, 2022, 3:40pm

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:

github.com/OpenChemistry/avogadrolibs

Fix crash reading non-standard PDB file

OpenChemistry:master ← ghutchis:fix-pdb-crash

opened 03:36PM - 01 Sep 22 UTC

ghutchis

+33 -21

Reported by teslim on the forum: https://discuss.avogadro.cc/t/avogadro-quit-un…expectedly/3953/5 Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com> 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.

teslim · September 1, 2022, 4:30pm

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

Avogadro2 error report

ghutchis · September 1, 2022, 4:44pm

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
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

teslim · September 1, 2022, 5:49pm

Thanks @ghutchis. I will follow your advice. Super appreciate it

ghutchis · September 2, 2022, 12:49am

The Mac build is here:
https://github.com/OpenChemistry/avogadrolibs/suites/8099621167/artifacts/349920174

You should also be able to use a “nightly build” from https://two.avogadro.cc/ fairly soon since the fix has been merged into the main code.