Can't open a .cif file in Avogadro

src · March 22, 2021, 11:27pm

I believe this to be a bug with Avogadro

Environment Information

Avogadro version: 1.93.0
Operating system and version: MacOS 11.2.3

Expected Behavior

I tried to open a .cif file.

Actual Behavior

I downloaded Avogadro from the following link (nightly.link | Repository OpenChemistry/avogadrolibs | Workflow build_cmake.yml | Branch master) but a .cif file does not appear as an acceptable file format when I try to open one.

Steps to Reproduce

ghutchis · March 23, 2021, 1:03am

Can you post a screenshot of what you do see in the list?

This is what I see on my MacBook from that version.

ghutchis · March 23, 2021, 1:04am

The default should be “All Supported Formats” or blank - either should open the CIF.

src · March 23, 2021, 3:04am

Here you go. As you can see, I don’t see an option for a *.cif file.

ghutchis · March 23, 2021, 3:54am

Huh. Those are built-in to Avogadro2, but none of the Open Babel formats are available.

If you Control-click the App you downloaded, there’s “Show Package Contents” and you can see the paths inside the binary. It should look like this:

Contents => lib => openbabel => many *.so files

In Contents => MacOS there should also be an obabel binary.

Assuming all of that checks out (and it should - we downloaded the same package), I’d want you to run it from the Terminal to see what kind of error messages come up, something like:

~  /Applications/Avogadro2.app/Contents/MacOS/Avogadro2

(Whatever the path to the Avogadro2.app bundle that you want to run. You’ll get something like this.)

Locale:  "en_US"
"/Applications/Avogadro2.app/Contents/translations"
Extension plugins dynamically found... 35
Checking for  "commands"  scripts in "/Users/ghutchis/Library/Application Support/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/Library/Application Support/OpenChemistry/Avogadro/commands"
Checking for  "commands"  scripts in "/Applications/Avogadro2.app/Contents/Resources/commands"
Checking for  "commands"  scripts in "/Applications/Avogadro2.app/Contents/MacOS/../lib/avogadro2/scripts/commands"
OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L formats read"
OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L formats write"
OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L forcefields"
OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-V"
"/Applications/Avogadro2.app/Contents/MacOS/obabel"  found:  "/Applications/Avogadro2.app/Contents/MacOS/obabel: Open Babel 3.1.0 -- Sep  6 2020 -- 15:40:59"

src · March 23, 2021, 4:21am

Thanks.

In Contents => MacOS there is indeed an executable “obabel”.

When I type in the terminal

~ /Applications/Avogadro2.app/Contents/MacOS/Avogadro2

I get an error message “zsh: permission denied”. Sorry for the block-headed message, but I’m new at this. Do you have any suggestion for a workaround so that I can check the error messages you suggested?

ghutchis · March 23, 2021, 2:02pm

I’ll guess that the various file formats were there under Contents => lib => openbabel as well?

Is that the path that you installed that build of Avogadro2?

Like if you left it in Downloads, it might be ~/Downloads/Avogadro2.app/Contents/MacOS/Avogadro

Put another way, you can save yourself some typing if zsh auto-completes the path for you.
/App + [tab] => /Applications => Avogadro2 + [tab] = /Applications/Avogadro2.app/

If you can tab-complete the path, you should be able to run the program from the Terminal.

If that doesn’t work, let’s find time to check this over Zoom. I’m really confused why it’s not finding the Open Babel formats and it’s kind of a problem (i.e., Avogadro2 will be missing a lot of features).

src · March 24, 2021, 2:55am

Thanks, Geoff. Okay, I was able to open Avogadro from Terminal. Here’s what I get:

“Error running script ‘/Users/runner/hostedtoolcache/Python/3.9.2/x64/bin/python3 /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/commands/scale.py --display-name --lang en_US’: Timed out waiting for finish (Script failed to start.).”

“Error running script ‘/Users/runner/hostedtoolcache/Python/3.9.2/x64/bin/python3 /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/inputGenerators/dalton.py --display-name --lang en_US’: Timed out waiting for finish (Script failed to start.).”

“Error running script ‘/Users/runner/hostedtoolcache/Python/3.9.2/x64/bin/python3 /Applications/Avogadro2.app/Contents/lib/avogadro2/scripts/inputGenerators/gamessuk.py --display-name --lang en_US’: Timed out waiting for finish (Script failed to start.).”

And a number of similar errors. Does that help?

If it’s still a mystery, we can zoom. Thank you so much for your willingness to help!!!

ghutchis · March 24, 2021, 3:57am

Thanks. Yeah, I’m not worried about those… Were there Open Babel comments in there like this?

OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L formats read"
OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L formats write"
OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L forcefields"
OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-V"
"/Applications/Avogadro2.app/Contents/MacOS/obabel"  found:  "/Applications/Avogadro2.app/Contents/MacOS/obabel: Open Babel 3.1.0 -- Sep  6 2020 -- 15:40:59"

If not, I guess I have a few ideas and will put together a debug build tomorrow.

src · March 24, 2021, 11:14pm

Yes, there were:

OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L formats read" OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L formats write" OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-L forcefields" OBProcess::executeObabel: Running "/Applications/Avogadro2.app/Contents/MacOS/obabel" "-V" "/Applications/Avogadro2.app/Contents/MacOS/obabel" found: "/Applications/Avogadro2.app/Contents/MacOS/obabel: Open Babel 3.1.0 -- Mar 17 2021 -- 18:57:57"

Looks like I can only upload images here, but feel free to email me (redacted) if you’d like a readout of all of the messages, or I can post it here even though it’s quite long.

Thanks again.

ghutchis · April 1, 2021, 10:44pm

I’ll send you an e-mail to see if we can figure this out. There will be a build with some debugging bits turned on from here:

github.com/OpenChemistry/avogadrolibs

Add some debugging to see if we can work out Mac OB issue

OpenChemistry:master ← ghutchis:debugging-ob-formats

opened 10:43PM - 01 Apr 21 UTC

ghutchis

+6 -2

https://discuss.avogadro.cc/t/cant-open-a-cif-file-in-avogadro/3447/10 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.

I’ll send the specific link in a bit.

ghutchis · April 6, 2021, 5:34pm

Okay, here’s the link if you can try running this from the Terminal:
https://github.com/OpenChemistry/avogadrolibs/suites/2403710835/artifacts/51172251

myoung · July 6, 2021, 3:56am

Just wanted to piggy back here to note that with v. 1.94 I am seeing exactly the same thing as src (with MacOS Mojave).

ghutchis · July 6, 2021, 4:19am

Please try the latest nightly:
https://nightly.link/OpenChemistry/avogadrolibs/workflows/build_cmake/master/macOS.dmg

I think we’ve ironed out all of those issues, but would like to know for sure.

myoung · July 6, 2021, 4:43am

I can verify that CIF files are an option in the file type list and I can open them in this build. Thanks for the prompt reply.
Now, off to figure out how to build some supercells.

myoung · July 6, 2021, 6:10pm

One difference I see is that in v1.20, the Super Cell Builder function adds atoms with the bonds displayed. In v1.94 (Avogadro2) using the Build Supercell adds atoms without bonds (the only bonds showing are for the original unit cell). I can select Bond Atoms but, with the default parameters, unphysical bonds are added (e.g. Ti-Ti bonds in TiO2).

ghutchis · July 6, 2021, 6:23pm

Could you please file an issue for the bonding (e.g. give an example file for the Ti-Ti bonds).

myoung · July 8, 2021, 4:22am

I made an account and did that, however inelegantly.