556. Briefly: Drawing molecules on linux: ghempaint, chemtool and easychem

chemtool, easychem and gchempaint are in the Wheezy repos.
See also the following posts for ISISDraw, MarvinSketch and BKChem.

Chemtool
I didn't get along with this at all. I managed to import a few structures from the templates, but e.g. the clean molecule function didn't actually work, although it's there. Selecting, deleting etc. were all a bit non-intuitive (to me -- this is obviously very subjective)

Easychem
I can't find any templates. Drawing becomes a bit tedious since I didn't find an easy way of converting an existing bond from e.g. single to double.

gChemPaint
It's pretty straightforward to use and I like it the best of the three. However, it's still very sparse even compared to e.g. bkchem. It certainly works if you quickly need to make a simple structure. There's no clean function.

555. Very Briefly: Drawing molecules on linux: bkchem

I can't evaluate drawing programs on linux without giving bkchem a look. In fact, up till now this has been my preferred drawing application on linux, in particular since it uses .svg as it's native file format i.e. it's very easy to post-process drawing and turn them into proper .eps files for inclusion in latex documents.

bkchem is in the debian repos:

sudo apt-get install bkchem

It's a very basic program, although looking through the options it isn't too feature sparse either.

However, there's one important feature that ISISDraw and MarvinSketch have that I can't find in bkchem: it's lacking a function to clean molecules i.e. to make them look nice.

554. Briefly: Drawing molecules on linux: Marvinsketch

I don't remember how I installed this, but marvinsketch is by far the fanciest molecular drawing application on linux. It's written in java, which means that it runs natively (well, as natively as something like java can run).

Note: it's free for academia only and you will need to register.

To get MarvinBeans, go to https://www.chemaxon.com/ and register as an academic. Then go to http://www.chemaxon.com/download/marvin-suite/ and download the 64 bit linux installer with jre.

Presumable you can install it by doing

sh marvinbeans-6.1.0-linux_with_jre64.sh

in the download directory.
Once it's installed create a file called ~/.local/share/applications/marvinsketch.desktop:

[Desktop Entry]
Name=MarvinSketch
GenericName=MarvinSketch
Comment=Software for drawing molecules
Exec=sh /home/me/ChemAxon/MarvinBeans/MarvinSketch
Terminal=false
Type=Application
Categories=Science
Version=6.1

You should now be able to find it in GNOME 3.

There are a lot of similarities between ISISDraw and MarvinSketch -- and that's a good thing since it allows people like myself to draw molecules quickly without thinking too much about it.

A Blank slate

Running Chem Inspector

It didn't like my wedges

I turned the structure into 3D and rotated it

Elemental analysis