If you’re willing to try the AppImage, here’s a current build from the pull request: AppImage
The PDB above is 6vxx (~25k atoms) but we’re as much concerned with “if you’re doing normal editing or loading other molecules, is it distracting?” as “how does it look on a protein and how fast is it”
Other potentially interesting structures: 2DN2 = human hemoglobin ~5k atoms 5XNL = Photosystem II (~99k atoms) … I start to notice slight lags on debug builds
@ghutchis I was not as much successful as @seal with the AppImage in Debian 12/bookworm and Xfce 4.16. For example, I downloaded pdb2dn2.ent from https://www.rcsb.org and submitted this, as well its conversion into a .pdb (by OpenBabel 3.1.1) to the program; for both I may access the ball-and-stick representation, and licorice however not the cartoon schemes:
With the same input files, there is no problem to display these e.g., in Jmol:
A second issue is the direction of light. As shown for glucose, it seems to point left/bottom (A, C), later from back left, high angle in the representation of the viewer
vs the one when exporting the representation, e.g. via povray and its subsequent .png:
Picking a “tunnel” in the 2dn2 model (the original .ent model file), for example – though retaining the orientation of the molecule vs. the observer – may document this, too:
Perhaps one could offer both the old color scheme as default, where the occlusion approach is offered as a higher level of representation. If so, an adjustable alignment of the light source were desirable. Accelrys once offered a light-weight viewer for Windows where one can direct this in regard to the objects displayed:
With a new user profile in Debian which previously never used a version of Avogadro – neither from a .deb, nor an AppImage – the situation improved to the extent that I’m now able able to see visualize the cartoons. So far, I wasn’t able to figure out if/how/why “the other Avogadro” (an AppImage officially released as 1.97.0 prior to 2022-07-26) still used in the primary account, or remains of Avogadro installed via .deb and synaptic interferes with the new AppImage for testing.
What however is puzzling (but maybe it is by design) with the new AppImage (as in the report by August 25) in the new/clean Debian account is that choosing either style (ball and stick, cartoon, chickenwire) on the right hand side sometimes work by pressing the left-hand mouse button (three button mouse) as anticipated but then, returning to the canvas to rotate the structure, the setting snaps back into the previous state:
To improve this report, the screen cast now includes the report by screenkey in the lower part of the .gif.
This interferes with the inspection (pen-rose mode, instead of construction/pen mode) of the structure.
For me, even more puzzling is the observation that on occasion, the space bar seems to alter the state (when the section on the right still is highlighted in blue) as toggle-on and toggle-off.
While submitting the 99k atom model 5XNL to Avogadro, the program suddenly closes; I speculate this requires briefly more than 4GB RAM currently at disposition. Since neither one of the three .ent, or OpenBabel converted .pdb files are problematic for read and visualization by Jmol, the larger the structure to display (by total atom count), the more likely I am going to use Jmol instead of Avogadro when facing lesser performant hardware.