Molecule display has a black hole in its center

mariogutfilen · April 17, 2023, 12:52am

I believe this to be a bug with Avogadro

Environment Information

Avogadro version: 1.2.0
Operating system and version: Win10

Expected Behavior

I should be able to fully view and manipulate my molecule once it’s build

Actual Behavior

When I enter the molecule coordinates in “build” below, the molecule displayed has a black hole in its center. I can’t view all the atoms. Some of them do show up when rotating the molecule, but others disapear.

Steps to Reproduce

Enter the following xyz coordinates (atomic units) in build - cartesian coordinates and apply:

-0.63099212433774 7.66011582532215 8.43754198757045 au
7.09021578151115 2.96721514048735 8.43754198757045 au
6.13391226592148 9.27613090082026 2.56829829559705 au
-2.51626083129481 11.10997070957474 0.71036791286223 au
-6.92664160705726 8.70017932128745 2.56829829559705 au
-7.48019036098537 1.76699679732270 8.43754198757045 au
5.01298646488253 -5.82627601656768 8.43754198757045 au
10.71760787140662 -2.96721514048735 2.56829829559705 au
9.78864268003922 5.82627601656768 0.71036791286223 au
10.37967075623465 1.92715164452205 4.33776000275771 au
9.53008135339174 4.54191896301022 -4.33776000275771 au
-4.46619272647417 7.50913410349757 -7.34395451075375 au
-9.78864268003922 5.82627601656768 -0.71036791286224 au
-5.76148146823123 6.56805174656452 7.34395451075375 au
1.37466453028155 10.46717611861015 4.33776000275771 au
-1.37466453028155 10.46717611861014 -4.33776000275771 au
-11.34377739833948 1.04006349596530 0.71036791286223 au
-10.41481220697207 -3.89912437204563 2.56829829559705 au
-3.99201976107057 -6.56805174656452 8.43754198757045 au
0.48993367670122 -11.10997070957474 2.56829829559705 au
8.56597471128691 -7.50913410349757 0.71036791286223 au
5.04032478910479 -9.27613090082027 4.33776000275771 au
7.26457872222924 -7.66011582532215 -4.33776000275771 au
5.76148146823123 6.56805174656452 -7.34395451075375 au
2.51626083129481 11.10997070957474 -0.71036791286224 au
4.46619272647418 7.50913410349757 7.34395451075375 au
4.43771909998472 -1.04006349596530 10.46386914216403 au
10.41481220697207 -3.89912437204563 -2.56829829559705 au
8.02698409939372 -3.44985488425259 -7.34395451075375 au
2.97885618377378 3.44985488425258 -10.46386914216403 au
-4.43771909998471 -1.04006349596529 -10.46386914216403 au
-10.37967075623464 1.92715164452205 -4.33776000275771 au
-7.09021578151116 2.96721514048735 -8.43754198757044 au
-10.71760787140663 -2.96721514048735 -2.56829829559705 au
-4.20152415252608 -1.76699679732270 10.46386914216403 au
2.36048978335609 3.89912437204563 10.46386914216403 au
6.92664160705727 8.70017932128745 -2.56829829559705 au
-2.36048978335608 3.89912437204563 -10.46386914216403 au
-8.52174037349983 -1.92715164452205 -7.34395451075375 au
-8.56597471128691 -7.50913410349757 -0.71036791286224 au
-8.02698409939372 -3.44985488425259 7.34395451075375 au
-9.53008135339174 4.54191896301022 4.33776000275771 au
-4.49457916169184 -10.46717611861015 0.71036791286223 au
-7.26457872222925 -7.66011582532215 4.33776000275771 au
-5.04032478910479 -9.27613090082026 -4.33776000275771 au
11.34377739833948 1.04006349596530 -0.71036791286224 au
8.52174037349983 -1.92715164452205 7.34395451075375 au
0.38217145295906 -4.54191896301022 10.46386914216403 au
-0.48993367670122 -11.10997070957474 -2.56829829559705 au
-0.80053246765094 -8.70017932128745 -7.34395451075375 au
4.20152415252608 -1.76699679732270 -10.46386914216403 au
0.63099212433773 7.66011582532215 -8.43754198757044 au
-6.13391226592148 9.27613090082026 -2.56829829559705 au
-2.97885618377378 3.44985488425259 10.46386914216403 au
0.80053246765095 -8.70017932128745 7.34395451075375 au
4.49457916169184 -10.46717611861015 -0.71036791286224 au
3.99201976107057 -6.56805174656452 -8.43754198757044 au
7.48019036098537 1.76699679732270 -8.43754198757045 au
-0.38217145295906 -4.54191896301022 -10.46386914216403 au
-5.01298646488253 -5.82627601656768 -8.43754198757044 au
-3.57696788811665 -11.00877518226114 5.78765561963967 au
3.57696788811665 -11.00877518226114 -5.78765561963967 au
11.57531123927933 0.00000000000000 -5.78765561963967 au
3.57696788811665 11.00877518226114 -5.78765561963967 au
-9.36462350775631 6.80379723714370 -5.78765561963967 au
-11.57531123927933 0.00000000000000 5.78765561963967 au
0.00000000000000 0.00000000000000 12.94159139587296 au
9.36462350775631 6.80379723714370 5.78765561963967 au
-3.57696788811665 11.00877518226114 5.78765561963967 au
0.00000000000000 0.00000000000000 -12.94159139587296 au
9.36462350775631 -6.80379723714370 5.78765561963967 au
-9.36462350775632 -6.80379723714370 -5.78765561963966 au

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

ghutchis · April 17, 2023, 5:19pm

Your molecule is being clipped. When you set up a 3D view, Avogadro has to define the “front plane” (and back) for the system.

I’d suggest saving to a file (e.g., .xyz) and opening again. You’re right that the coordinate editor should rescale the clipping planes, but that should work for a temporary workaround.

mariogutfilen · April 17, 2023, 9:24pm

I made a script that turns these bohr unit coordinates into angstrom and makes a .xyz file.

When I tried reading my .xyz file, the molecule is quite strange, not looking at all like it should. I noticed in the build tab that the coordinates are strange

EDIT: I double-checked and my script wasn’t working properly. I can now correctly view my molecule

Au72.xyz (4.3 KB)

ghutchis · April 18, 2023, 12:27am

I’ll also point out that the Coordinate Editor in Avo2 is a bit more flexible and doesn’t seem to suffer from the clipping issue. I pasted your coordinates in (xyzS for x y z symbol) as Bohr, and set the display to VdW spheres: