nbehrnd

Hi @tccyl in short, after passing the `.pdb` to openbabel, the RMSD `calculate_rmsd.py` determines for either variant of the Kabsch test equals to about 0.7983. Below both the script's copy...

As by today (2021-04-24), I equally find it in the repositories of Debian 11 bullseye / sid (listed as version 0.18.0-0.1). Thus, an update of the gnome-pomodoro webpage currently stopping...

Depending on the depth to cover, I like to use [`tree`](https://tracker.debian.org/pkg/tree) because it discerns folders and files (folders may be disabled by `-d`) and yields a representation from which one...

I can replicate your findings with OpenBabel 3.1.1 (dfsg-6+b1) as provided in Linux Debian 12/bookworm (branch testing). To recover the geometries _at all_, I recommend [Jmol](http://jmol.sourceforge.net/) as an alternative; here,...

Based on the «steps to reproduce» shared by you, it seems plausible you missed an explicit space between `-O` (uppercase o) and the file to store the result as permanent...

If you want to continue with .pdb about individual models, use the .pdb by the database and split it into multiple files, each about one individual model. In openbabel, the...

The structure record is about a sample in solution characterized by solution NMR. Thus, though there is the provision of a .cif by the database, it isn't a .cif like...

As a general note: With version 2.3.2, you are using a very old version of OpenBabel. Consider to transition the current branch 3.1.1 (e.g., [online](https://open-babel.readthedocs.io/en/latest/index.html), or [the latest version as...

Just about `--gen3d`: this is a handy abbreviation to perform *an* optimization as if there were nothing (no solvent, no bulk, no ligand; but uniform vacuum) around the molecule of...

> Ok, now I realise the difference between the two options. > I will confirm by comparing coordinates generated by both methods. If the initial conformation as well as the...