Avogadro 1.102.0 can't display ORCA output

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1

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I believe this to be a bug with Avogadro:
Latest(?) version 1.102.0 gives an empty molecule when it reads ORCA output *.out

Environment Information

Avogadro version: 1.102.0
Operating system and version: Windows 11

Expected Behavior

I see the molecule, along with the vibrational frequencies dialog box, when I open the file using Avogadro2.

Actual Behavior

First, Avogadro tells me to download the latest version, which has the same numbers as the current version. (This apparently is a known bug). I choose Ignore.

Then, Avogadro asks me for Python. I download and install it.

Then, after a longer than usual wait, I get the vibrational frequencies dialog box and a BLANK molecule-view window. It’s not just black-on-black because if I change the background color, the molecule is still not being shown.

I suppose the molecule is being read after all, because if I export the molecule as ORCA input, I get a file that does contain all the atoms:

#ORCA input file

#
! insert inline commands here

*xyz 0 1
C -5.92272 2.71666 -0.00054
N -4.65600 2.70564 -0.00293
N -6.65895 1.57773 -0.01523
H -6.53437 3.62295 0.01326
H -6.18583 0.69114 -0.02851
H -7.65930 1.60107 -0.01317
H -4.27992 3.64562 0.00961

*

It’s just that the molecule isn’t being rendered on the screen, so I can’t view it or make changes.

Steps to Reproduce

I open an ORCA output file with Avogadro2 by right clicking and using the Open with command, then proceed as described in Actual Behavior.

Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)

2

Can you share a screenshot? What display types do you have enabled?

If you choose “download by name” and pick caffeine or something, do you see something?

If you draw something, do you see the atoms?

3

I forgot to mention that I read in a .cjson file and it worked fine. I could see the molecule.

I can also get a molecule to appear with build > insert > molecule, or by drawing from scratch. It appears to be just ORCA files that don’t work.

4

I can’t reproduce this. Can you paste a link to a file?

It would also really help if you could post a screenshot.

5

OK here are the output file and screenshot.

NH2-CS-H.out (393.1 KB)

Screenshot 2025-10-25 194136
Screenshot 2025-10-25 1941361920×1095 82.8 KB

6

I was kinda hoping to see the list of display types in your screenshot.

I opened it on my son’s Windows 11 box and it looks fine. Looks good on Mac too.

Please check to make sure that the Ball and Stick is enabled - and check the … icon to make sure the opacity is turned up. (Had a student with that problem last week.)

I understand it’s frustrating for you, but I simply cannot reproduce your bug, nor has anything related to that changed between 1.101 and 1.102 that I can tell.

7

OK, here’s another screenshot. I have tried some of the other display types, but I can’t get the molecule to appear.

Screenshot (2)
Screenshot (2)1920×1200 118 KB

8

I just discovered something. I idly selected View > Center and voila, part of the molecule appears at the edge of the screen, and I was able to select the entire molecule with ctrl-A and drag it to the actual center of the screen.

The molecule was there all along, just incorrectly placed outside the field of view!

FWIW, I am using Avogadro2 on a laptop’s built-in monitor, if that makes a difference.

1 Like
9

Great, glad you figured it out. Makes sense, honestly.

The other useful command is “unfocus” (even if you haven’t used “focus” previously)

The monitor / laptop doesn’t matter much. There is some code in 1.102 that tried to keep the camera view consistent between files, so that’s possibly the cause? :man_shrugging: