Since there is no answer after one week for resolving the part of the visualization using Avogadro, I show an approach for visual inspection of conformers generated by OpenBabel (version 3.1.1) with Jmol.
For dibenzylether (SMLES string C(c1ccccc1)OCc1ccccc1
is one description), I create a 3D model including hydrogen atoms which subsequently serves as reference to generate up to 1000 conformers:
obabel -:"C(c1ccccc1)OCc1ccccc1" -h --gen3d -osdf -O start.sdf
obabel start.sdf -O conformers.sdf --confab --conf 1000
which yields (with the implicit, yet adjustable defaults) 17 conformers in total.
File conformers.sdf
may be read by Jmol either at launch (jmol conformers.sdf &
), or from the CLI of the program itself (load "conformers.sdf";
) if the program already runs in the directory with this file. Note that the console recalls the history of your commands; instead of retyping, use arrow up and arrow down to recycle these commands.
You may display the individual conformers by their entry number (e.g., model 1
, model 2
, etc.). If you recall individual ones to be displayed simultaneously, e.g. for a pairwise comparison, use
model 0 # a reset to access all models in the .sdf
display 1.1, 1.4; # first and fourth model
display 1.2, 1.3; # second and third model
If you want to display a range of them (they must be back-to-back in the .sdf file read), use e.g.,
display * # reset previously set constraints by previous selection
model range 1.1 1.10 # note: neither comma, nor hyphen
model 0 # display the new selection
to display the first 10 entries in the file.
The discern of the molecules may be eased if these are coloured uniformly. Either use predefined colours or define them in RGB, e.g.
select model = 1; color red;
select model = 2; color {0, 0, 150};
# revert to original scheme:
select all; color cpk;
As an illustration: