I believe this to be a bug with Avogadro
Environment Information
Avogadro version: 1.97 (md5sum Avogadro2.AppImage.zip
used yields 45cd784ae051f447c6697fad6d870e87
, it was fetched from GitHub a couple of days ago).
Operating system and version: Linux Debian 12/bookworm
Expected Behavior
Smooth and continuous (i.e., closed) van der Waals surface.
Actual Behavior
On occasion, there are gaps in the surface (like the dials on the old mechanical telephones). Assuming these would be because the point of observation is too close to the surface, I pivot the model of pyridine (vide infra). However, the gaps on the upper and lower hemisphere (i.e., both on the front as well as the back) of the model remain visible.
Steps to Reproduce
Very similar to Gigux’ initiated thread:
-
File → import by Name →
pyridine
-
analyze → create surfaces. Parameters used are:
- Surface: van der Waals
- color by: electrostatic potential, EEM
- colormap: balance
- resolution: automatic
- isosurface: 0.0300
- smoothing: medium
-
The computation did not report an error back to the GUI. The display types used (earlier report/thread initiated by Gigiux) only are i) Ball and Stick, ii) Close Contacts, and iii) Meshes. The red straight lines are added by me after the export of the .png by Avogadro: