Lindqvist -- a blog about Linux and Science. Mostly.: molecules

Showing posts with label molecules. Show all posts

18 February 2014

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

553. Briefly: Drawing molecules on Debian Wheezy: ISISDraw under wine (very briefly)

I'm cheating here: this isn't a program for linux. Instead we're running a windows program under wine, which is not ideal. On the other hand, it's so easy to do that it's worth exploring as an option to 'pure' linux offerings.

I'll be posting about native linux offerings later.

Either way, I've kept a copy of ISISDraw 2.5 around since the early 2000s. Luckily, other people are mirroring the installation file for it as well. See e.g. http://fc.smcdsb.on.ca/~rszerminski/addl_files_for_web/DRAW24.EXE for ISISDraw 2.4

You'll need to install wine:i386 and for that you'll need to enable multiarch if you're on amd64:

sudo dpkg --add-architecture
sudo apt-get update
sudo apt-get install wine:i386
wget http://fc.smcdsb.on.ca/~rszerminski/addl_files_for_web/DRAW24.EXE
wine DRAW24.EXE

As always, if you have problems with e.g. weird fonts, use winetricks to install at least corefonts, or ideally allfonts:

wget http://winetricks.org/winetricks
sudo mv winetricks /usr/bin/winetricks
chmod +x /usr/bin/winetricks 
winetricks allfonts

Then run ISISDraw:

A blank slate

ISISDraw has a lot of options, including templates and journal settings.

Chem Inspector

There's a bug under wine: to get the menus for the buttons on the left side to show up, click on the button on the left panel, and then move the mouse left while still holding the button down.

To get the menus to work, click and while still holding the left button down move right

ISISDraw is not going to blow you away, but it's free and it works under wine.

01 March 2012

87. Polyoxometalate Molecules - povray images

Here's a bunch of povray generated figures of polyoxometalates. I've spent too much time on them not to share them. You may use them freely in posters, websites or talks.

Leave a comment if you want the original POV files.