557. Briefly: Drawing Molecules on Linux: ACD/ChemSketch in Wine

This is another post where I'm cheating a bit -- this is a windows program running in wine.

Let me explain. Sometimes you absolutely need to get a task done -- I use linux at work and I can't not do something just because I can't write/find a piece of software that does it for me. Science is the goal, and the route there is immaterial. So sometimes you need to be pragmatic about your software choices.

I much prefer to use free and open source software since it allows me to keep a copy of the source code which I can recompile in case the prebuilt binary suddenly won't work with a future version of debian. Having the source makes me feel more secure in the assertion that it's worth my time learning how to use that piece of software.

Second to that, I prefer native linux software -- although unfortunately 'native' here often means 'written in java', and -- while not knowing too much about java -- from a user point of view java software tends to be comparatively slow to load and run. Certainly it appears slower than a comparable C/C++ program.

As a last resort, I can accept having to run a windows binary in wine. It doesn't make me happy, and often there are small, niggling issues associated with it -- but if it can get the job done, so be it.

Note that I'm unwilling to actually run a native windows program on a native windows installation -- one has to have some standards...

Either way, this is why I look at windows programs as well for drawing structures and processing NMR spectra.

So I recently tested marvinsketch (linux), bkchem (linux), easychem (linux), chemtool (linux), gchempaint (linux), ISISDraw (wine) and ChemSketch (wine). Out of those I prefer MarvinSketch. However, I'm still exploring the alternatives.

ACD/ChemSketch for Linux is really just an older (2006) version of ACD/LABS free ChemSketch (the windows version is from 2013). To get it, go to http://www.acdlabs.com/resources/freeware/index.php and click on Download. I tried the version 'for linux', and not the windows one. I'm making the presumption that the newer binary won't play well with wine.

You don't need to be an academic to qualify for the free version.

wine ~/Downloads/chemsk50.exe

Once it's installed you can explore ChemSketch. Overall it's fairly similar to e.g. ISISDraw.

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.

498. Briefly: Drawing NMR pulse sequences using APSEQ and Mathematica

There are two things that have been bothering me on linux -- one is the difficulty of creating annotated PDF documents, but it seems like things are slowly improving (we still don't have a really good way of creating /editable/ annotations). Another is the issue of creating NMR pulse-sequence drawings. To be fair, it doesn't seem like the situation is much better on Windows or OSX.

Anyway, I still don't have a good way of doing this, but at least I have A way of getting it done: APSEQ. The main drawback is that it requires Mathematica, which I don't like much (I get by with octave and maxima) in addition to being proprietary. But it will do for now.

NOTE: I just needed to 'Get It Done' quickly, so I didn't spend any time looking at the following potential alternatives:
http://www.celos.net/comp/pulses/ (metapost -- which should be tex compatible, right)
https://code.google.com/p/nmrtype/ (python code)
http://nmrwiki.org/wiki/index.php?title=NMRPulse_-_pulse_sequence_drawing_extension_for_MediaWiki (the URL is fairly descriptive)
They all seem to depend on latex in some way or another.

There's also http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.187.9656&rep=rep1&type=pdf but I haven't actually found the sources.

Anyway, here's how to get started with APSEQ:

mkdir ~/tmp/apseq -p
cd ~/tmp/apseq
wget https://www.princeton.edu/~nmr/apseq/apsDistribution.tar.gz
tar xvf apsDistribution.tar.gz
cd zip.feb15/
math

Mathematica 7.0 for Linux x86 (64-bit)
Copyright 1988-2009 Wolfram Research, Inc.

In[1]:= <<nmr.auto
part01 loaded
part02 loaded
part03 loaded
part04 loaded
mscp loaded
nmr.extra loaded
nmr.auto loaded

In[2]:= draw[pulseSeq[hahn, echo]={channels[1H],pulse[90],delay[t1],pulse[180],delay[t1],delay[t2],acquire[taq]}]

Out[2]= hahn_echo.pdf

In[3]:=

which gives you something like this:

Spin echo sequence

The figure is output as a pdf, but it's easy enough to open it in inkscape and converting it to an .eps file.