Avogadro 1.98 reads Zinc as Calcium?

JDoe · November 13, 2023, 1:04pm

I’m looking at my ORCA outfiles right now and it seems like avogadro thinks that Zinc is supposed to be Calcium for some reason. Not just that, but another input file shows Iodine as Nitrogen.

The bond orders are also wrong. I made a comparison between Avogadro 1.20 and 1.98 to verify that it is in fact an issue with 1.98. I’m guessing 1.98 is still rough around the edges for ORCA 5.0.4 files?

Comparison:

Environment Information

Avogadro version: 1.98
Operating system and version: Windows 11

Files

ghutchis · November 13, 2023, 3:20pm

The Orca code is definitely new, but swapping elements is truly weird.

As far as bond orders, it’s also somewhat newer code, but it’s also going to be confused by the initial bonding (e.g, if you have a bond to a “Zinc” that top carbon already has 4 single bonds, so it won’t create a double bond to the nitrogen, etc.)

ghutchis · November 13, 2023, 3:30pm

Okay, that was an easy fix - thanks for the heads-up. (But a bit confused when the “Br” files contained Cl, not bromine!)

github.com/OpenChemistry/avogadrolibs

Fix atomic numbers from Orca - it would read electrons not symbols

OpenChemistry:master ← ghutchis:fix-orca-elements

opened 03:29PM - 13 Nov 23 UTC

ghutchis

+3 -1

Thanks to the forum https://discuss.avogadro.cc/t/avogadro-1-98-reads-zinc-as-c…alcium/4978 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.

JDoe · November 13, 2023, 4:15pm

yeah I have a lot of these files and I uploaded only two. looks like I fat-fingered the log files and grabbed the wrong one.

ghutchis · November 13, 2023, 4:37pm

No worries… I think we’ve all done similar things - just chuckled when I opened the file and saw chlorines… had to check the file itself.