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How to look at the same angle from conformers

is there a way in the windows version 1.2 to always look the molecules (conformers) from the same perspective;
like I could fixed a cycle, and I could see the different stuff around moving…

also in Obabel is there a way to sort them out by a dihedral angle bond, for example between 50 to 110 degres…


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:


Thanks a lot will have a look at Jmol,
It is linux only?

@galojoute13 If you want to use Jmol, you only need a Java run time environment between the operating system and the program (does not matter if it is Windows, Mac, or Linux). OpenJDK is an example for this moderating layer. (Since you do not want to write new Java programs, you do not need a Java development environment.) You may check if the installation of Java was successful if the command java -version on the cmd.exe/the command prompt of Windows yields something similar to

openjdk 11.0.13 2021-10-19

Then, download the .zip archive from sourceforge (at present, Jmol-14.31.60-binary.zip, 56 MByte) and decompress it anywhere on your computer to a place where you may retrieve it later.

The Java version of the program is within Jmol.jar. If a) your computer recognizes files with the extension .jar as Java executables, then a double click with the mouse will launch the program. Then, you are set to venture out, e.g., the documentation with its tutorials.

If a) is not successful, b), enter the folder containing Jmol.jar with cmd.exe and launch the program with the command java -jar Jmol.jar from the terminal.

thank you Thomas will try it soon, cheers