# log how to change a molecule's orienation

Following a request to change a molecule's orienation in respect to outer
coordinates, I identify the implementation
[orient-molecule](https://github.com/smparker/orient-molecule) by Shane M.
Parker worth a try.  Implemented in Python2 but set up to work out of the box
with contemporary Python 3.11.2.  Depends on the standard library `math` as well
as the non-standard `numpy` (version 1.24.2 appears to be compatible).  License
is GNU GPL v3.

## preparation by openbabel:

With Debian 12/bookworm (Open Babel 3.1.1 -- Jan  4 2023 -- 09:58:24)

``` shell
$ obabel -:"CCOCC" -h --gen3d -O diethylether.xyz
```

## rotation with orient-molecule:

With bash (5.2.15(1)-release (x86_64-pc-linux-gnu)) and Python (3.11.2)

``` shell
python3 ./orient.py -rz 90 ./diethylether.xyz > rz90.xyz
```

## processing in Jmol 16.1.7 (2023-03-08)

I use Jmol 16.1.7 (2023-03-08) from sourceforge.  From Jmol's console (File ->
Console)

``` javascript
load files "diethyether.xyz" "rz90.xyz"
// (replace the file's name with the complete unique path, e.g.
// ~/Desktop/diethylether.xyz)
select 1.1; color red;  // about the first model entry in the first data file
select 2.1; color blue; // about the first model in the second data file

// simultaneous display of both models
model 0;

// generation of a permanent record:
write "example.png"
```

END