About this Author
DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

Chemistry and Drug Data: Drugbank
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
Not Voodoo

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
Realizations in Biostatistics
ChemSpider Blog
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Eye on FDA
Chemical Forums
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa

Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
Gene Expression (I)
Gene Expression (II)
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net

Medical Blogs
DB's Medical Rants
Science-Based Medicine
Respectful Insolence
Diabetes Mine

Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem

Politics / Current Events
Virginia Postrel
Belmont Club
Mickey Kaus

Belles Lettres
Uncouth Reflections
Arts and Letters Daily
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

In the Pipeline

« Sulfolane | Main | The Novartis Pipeline »

November 19, 2012

ChemDraw Magic

Email This Entry

Posted by Derek

Via a reader, here's an excellent YouTube video for those of you who use ChemDraw. I've been using the software since it came out, and there are several useful tricks here that I didn't know were even in the software. Did you know that you could give your common structures nicknames, so that the program would immediately draw them when you typed in the name? Or how to use the "Sprout" tool for drawing bonds without going to the bond-drawing tool? There's also an detailed look at customizing hotkeys, which for a heavy ChemDraw user will make you look like you have magic powers. Well worth a look. Update: see the comments for more if you're into this sort of thing!

I'd still like to see how quickly all these would allow you to draw something like this (well, other than giving it a nickname - I'd suggest "Jabba" or "Chemzilla" - and having it appear instantly). Of course, those of us old enough to remember the pre-ChemDraw (or any-other-draw) days will have a different perspective on the whole field. I remember the first time I saw the program being used, which would have been 1986, not an awful long time after it came out (see the timeline of computers in chemistry here). Like every other practicing organic chemist, as soon as I saw the program I knew that I had to have it. It was, as they say, a "killer app", and ChemDraw sold Macs, albeit on a smaller scale than VisiCalc sold Apple IIs. But it's hard to get across how those programs felt, unless you've actually rubbed Helvetica capital letters from a transfer sheet into an ink-drawn chair-conformation ring to make a drawing of a carbohydrate, or had to go back and manually erase (and write in) half a column of figures because you had recalculate them. It feels like, instead of hitting "Print", being given instead a slab of hardwood and some sharp tools which which to start carving out a block for inking. Or instead of hitting "Send", having someone bring you a horse.

Comments (33) + TrackBacks (0) | Category: Chemical News


1. Trashbagel on November 19, 2012 9:24 AM writes...

I love Chemdraw but the price is so high it's hard to justify unless you draw as much as you e-mail.

Permalink to Comment

2. Thomas McEntee on November 19, 2012 9:28 AM writes...

Helvetica letters from a transfer sheet? What's a transfer sheet? Don't people still use Rapidograph pens with the West German lettering stencils for all text characters in their structures? My dissertation on synthetic approaches to the Cinchona alkaloids (this was the late 1960s, there was a war going on, and the plasmodiae had become resistant to classic antimalarials) relied on the use of these. One smudge and it was back to the IBM Selectric to re-type the entire page and try again.

Permalink to Comment

3. cookingwithsolvents on November 19, 2012 9:29 AM writes...

I know some tricks but nothing like the later stuff. FANTASTIC!

Permalink to Comment

4. Bauke on November 19, 2012 9:39 AM writes...

too bad he's NOT drawing Trp...

Permalink to Comment

5. A Nonny Mouse on November 19, 2012 9:40 AM writes...

We had the fist chemical drawing programme for Windows (3.1.......) which was done in 1984-85 by one of the chemists in his spare time ("Moledraw"). Several companies were interested in purchasing it, but the company would not allow it. Management took offence when he programmed a mole to pop its head up every so often. Later abandoned when the commercial programmes came along.

Permalink to Comment

6. petros on November 19, 2012 9:45 AM writes...

I've used stencils,
chemical letraset- Aldrich sold sheets of benzene rings, sugars etc,
WIMP (using an inkjet to print)
MDL's Chemdraw & Chemdoc - essential for camera ready BMCL MS!
IsisDraw and its later incarnations

but never the Cambridge Soft ChemDraw

Permalink to Comment

7. road on November 19, 2012 10:14 AM writes...

Thanks for the post!!! -- I've been wondering how to draw bonds from the keyboard (SPROUT) for years...

Permalink to Comment

8. luysii on November 19, 2012 10:38 AM writes...

Are there any publicly available chemistry drawing programs around for the Mac, for someone whose love of organic chemistry, while intense, doesn't reach the $1500 level?

Permalink to Comment

9. Chemjobber on November 19, 2012 11:01 AM writes...

@8: There's the free version of ChemSketch, which is clunky.

I've been playing around with ChemDoodle all weekend, and have been pretty happy with it. Free, but a lifetime license is $70.

Permalink to Comment

10. Anon on November 19, 2012 11:10 AM writes...

Are cambridgesoft ever going to sort out compatability issues with office on mac?

Permalink to Comment

11. John Wayne on November 19, 2012 11:35 AM writes...

@10: I doubt it. I work for a small Mac-based company. Everybody who has Chemdraw has some stability issues with their computer, while everybody without Chemdraw is just fine. There is something messy about how the program works on a Mac.

Permalink to Comment

12. Old Lab Rat on November 19, 2012 11:58 AM writes...

@ 8, try MarvinSketch from ChemAxon. Single user license is free, 99% of the features of ChemDraw and more chemically intuitive. It's very easy to save your own templates (draw, select, drag to template toolbar). Also, the developers are responsive to the user community. Not as good for organometallic complexes, but doable.

I've tried almost every drawing app available for the last 25 years. ISISDraw was the most efficient, ChemDraw allowed the fanciest sketches. MarvinSketch is the best compromise to date.

I don't work for ChemAxon, just like the application.

Permalink to Comment

13. BioBritSD on November 19, 2012 12:28 PM writes...

Hi Derek,
Full Disclosure first - I do actually work for PerkinElmer - who (for those who hadn't realized yet) acquired CambridgeSoft around a year ago and now owns ChemBioDraw (and E-Notebook, and Spotfire, and .....)

wrt creating shortcut keys for big ugly molecules - yes, that is a great way to do it. Another way however is to create your big ugly compound as a template. You can create your own templates (like the predrawn Cp rings, bicyclics, hexoses etc) that you get from the main toolbar or from the view menu. There is a how-to guide (and a host of other templates you can insert) on the website. These, as in fact so can hotkeys and shortcuts, be personal or shared institutionally.

The viagra example is interesting - you can actually draw that much faster than the youtube author - go to Structure/Convert Name To structure, type viagra into the dialog box and the structure appears. Of course, the techniques used in the video are more applicable outside of the included nomenclature library

@10 - have you reported this to support?

@1 - there are much lower price variants of ChemDraw. The full price version does have a lot more than drawing included - including a very robust set of rules on what constitutes a valid chemical drawing (as per IUPAC) or not. *You* may not need this, but these extra things (naming, structure clean up, NMR prediction, peptide/nucleotide handling, biology drawing, direct database access etc.) are desired by some and contributes to the full version pricing.

Permalink to Comment

14. BioBritSD on November 19, 2012 12:47 PM writes...

There are a few more "How To" video's here:

THanks for the link though - I learned a few new tricks too.

Permalink to Comment

15. TX raven on November 19, 2012 1:46 PM writes...

I used the Fieser triangle for my dissertation...
Still being sold by Sigma-Aldrich.

Permalink to Comment

16. Trashbagel on November 19, 2012 2:25 PM writes...

@13 Currently a ChemDraw Std 13.0 perpetual commercial license = $990.

In my opinion that is expensive when there are other packages that are free or lower cost. The additional costs for the other tools are reasonable but that base price is high. It is great software and I applaud you for having a list price on the web.

Another suggestion for others to consider is TouchMol and TouchMol for Office.

Permalink to Comment

17. lgf on November 19, 2012 3:35 PM writes...

so BioBrit, how do I get my personal vintage copy of ChemOfficePro 2005 to reinstall. My PUI buys a multi user license of the standard software every year, but it lacks the friggin clean up option, the one thing that makes me crazy to not have access to my full featured version. I just get serial number error messages, I need a reactivation code.

Permalink to Comment

18. David Formerly Known as a Chemist on November 19, 2012 4:08 PM writes...

These kids today and their fancy toys! I remember writing my thesis (1990) on an early IBM PC that didn't even have a hard drive. I had to load the word processing program (Volkswriter, haha) from two floppy disks (remember those?), then save my text file on a third floppy disk. There was no way to integrate structural formulas or reaction diagrams into the file, so one would need to leave a gap in the text and print out a page. The chemistry drawings were then drawn in the gaps using plastic templates with a good quality ink pen. The bound copy of my thesis has that quaint old-timey look. I remember hearing of this thing called "ChemDraw" back around that time, but don't remember ever seeing a working version until my postdoc days.

Permalink to Comment

19. BioBritSD on November 19, 2012 4:17 PM writes...

@Igf - contact support. This site is the best although you can email or phone also. Probably something to do with registries - out of my knowledge area, but then that is why you should contact support.
Note that depending on the terms of your license, or if you kept up with maintenance, you may be out of support -2005 is pretty old - or your version might not be compatible with your current OS. You can buy one off tickets though if that is the case.

Permalink to Comment

20. lgf on November 19, 2012 4:33 PM writes...

thanks, BioBrit. contact/support seemed like a sinkhole to me - the software is old. However, I am not asking for it to perform any better than it did when I purchased it. Since my car does not get unplugged after 7 years, I hoped to keep my software running. Our shared problems emanate from the fact that IT fails to actually fix problems, they merely recover data files and throw away software.

Permalink to Comment

21. BioBritSD on November 19, 2012 5:00 PM writes...

@Igf - and it should run the same as in 2005 - assuming everything else has stood still. If you are still running Windows NT or whatever it was back then, then great. Where we have often encountered frustration - to exaggerate the situation somewhat - is when people have bought a perpetual license of ChemDraw 15 years ago, finally upgraded their desktop from Windows 98 to Windows 7, and wonder why the software doesn't work any more.

I don't understand the inner workings of Windows, I'm just a synthetic chemist who has found a new career path. But, if you know your way around windows registry I'd start there. ChemDraw (and most software) is written to accomodate moving forward easier than moving back.

The other possibility is that the license key info isn't kept back that long for validating the installation. Just a wild guess. But support is the best way to resolve that if that is the case.

Permalink to Comment

22. Pugwash on November 19, 2012 5:40 PM writes...

If your constantly hitting Reaxys or similar to find related compounds, good software saves time every time. Yes, it IS expensive and Yes, it does have issues but how much is your time worth?

I do go searching a lot (5000+ hits per month) so maybe I'm using it more than some, but those free packages would cost me 3-4 days per month in lost productivity...

Permalink to Comment

23. Canageek on November 19, 2012 5:58 PM writes...

My dilemma: My uni pays for the very limited version of ChemDraw. It has some very nice features, and a nice interface. However, it doesn't come with some really basic stuff, such as structure cleanup.

Then there is ACD/ChemSketch, which has some of those features, including cleanup, but can't do 3D movement, and the figures aren't publication quality.


Permalink to Comment

24. r.pal on November 19, 2012 10:54 PM writes...

USe chem doodle cheap at $59 and as a previous chem draw user it more than replaces cehmdraw

Permalink to Comment

25. bad wolf on November 19, 2012 11:03 PM writes...

@Trashbagel--Chemdraw Std 13.0 Suite download perpetual english windows is $170 academic, which is the same as their home user price. Download one year = $60. Commercial prices assume a for-profit company user. So if your company is not paying for it those are reasonable for personal use.

That so many chemists use the program and so few pay for it may be related to the reason that Cambridgesoft was unprofitable and bought by PE.

Permalink to Comment

26. Anonymous on November 20, 2012 12:14 AM writes...

I have always been amazed at the comparatively small market share of ChemDraw compared to the ISIS/Symyx/Accelerys Draw competition(at least in industry). Over its entire lifespan from ISIS to Accelerys, the drawing program has been a joke. For a program that has been around for 22 years they still haven't been able to implement a properly working text tool. It amazes me that it is the de facto drawing program for so many companies.

Permalink to Comment

27. LiqC on November 20, 2012 2:22 PM writes...

Unfortunately, some of these command don't work in ChemDraw 10 and 11, namely ARROW and BRACKETS. Way back, I wrote about the hotkeys here:

A Cambridgesoft person commented on that post, from which you'd think they'are aware of the problem, and would fix it.

I downloaded CD 12 to check -- nope. I didn't find anything in CD 12 that was different from CD 11, other than that it was bloated to >1 GB. CD 13 is now over 2 GB, and I'm guessing things won't change either.

Permalink to Comment

28. Pugwash on November 20, 2012 4:46 PM writes...

I guess I use ChemOffice because it was the one everyone around me was using. Even more embarrassing, I don't know what the boss paid for the professional edition.

One thing I think is totally unacceptable is the technical support. If I try to twist a bond in ChemBio3D the program like-as-not crashes. I sent a detailed report with every bit of information I could think of and they wanted to arrange an on-line conference. Meetings are something that happens at weekends for me - weekdays I'm unable to just leave a big space 'for if'. I know other people have this problem so it isn't like they don't know the cause (if they don't then they need to replace the coders) so why no patch?

Any chance of an article on Discovery Studio, Derek? I keep meaning to get a 30 day trial but there is always something to do...

Permalink to Comment

29. Pugwash on November 20, 2012 4:49 PM writes...

BTW has anyone else noticed that the MM2 energy minimization can give totally different results each time you run it? That is REALLY helpful..

Permalink to Comment

30. Richard Blaine on November 20, 2012 4:52 PM writes...

You young whippersnappers cannot imagine what a boon it was to scientific publishing in the 1980’s to have the first computer drawing tools combined with a functional word-processing program. Before that, I had used the afore-mentioned Stadtler (sp?) ink drafting pens with a very expensive template I bought (and still own) from a German company, plus the rub-on letters from Aldrich. Believe me, these were painful to use.

I bought an early IBM PC when I was in grad school ca. 1983. Back then, you wrote most of your own software, so my very first program (written in Turbo Pascal!) was a chemical structure drafting program. It had very primitive capabilities (no mouse, everything done with the keyboard), but did print nice looking benzene rings either on a dot-matrix printer or (believe it or not) an HP pen plotter! Later, I wrote another program to draw simple Cartesian plots.

To write my dissertation, I used a stunning (for its time) commercial word processor called ChiWriter. It was designed by a math professor (IIRC), and was one of the first WYSIWYG word processors. Amazingly, it could typeset complex equations including multiple subscripts and superscripts, plus it had many fonts including bold, italic, and Greek!!

However, cutting and pasting was still literal, as Chiwriter could not incorporate graphics. I had to guess how much room was needed to fit a chemical structure or graph, leave a bunch of blank lines, and then glue the graphic in later. To construct my thesis document, I printed out the graphics in various magnifications, matched the reserved space between the lines of text to the right sized graphic, and then got busy with the scissors and glue.

Later, one of my lab-mates bought a Mac. Despite its pathetic screen and under-powered processor, it could (mirabile visu!) combine text and graphics right on the screen. This was the brilliant dawn to a new age. You really had to have been there to appreciate just how revolutionary this was.

Permalink to Comment

31. DrSnowboard on November 21, 2012 4:33 AM writes...

I second Chemdoodle if you need occasional use and paying for it yourself, it was the cheapest Mac option I found and works fine.
My final year project was typed with stencilled diagrams pasted in, fortunately after I realised my typist had put onion rather than anion throughout...
My thesis was on a Mac using Chemdraw. Heaven, except for having to write in shifts as only my supervisor had one.
Career was ISIS who only really cared about corporate clients and then decided to just drop everybody and go to Symyx, presumably due to OS changes they couldn't cope with. Support disappeared overnight - thanks guys! Cambridgesoft worked for a bit in a small biotech environment but never got comfortable with it. With web integration it was all about the browser tools , dotmatics which was great but....not for home use.

Permalink to Comment

32. NH_Chem on November 24, 2012 8:50 AM writes...

I have an old version that works fine. To upgrade is not worth it. Too expensive. This is the reason why so many people share their serial numbers. Lower the cost for individual owners and they would have more business.

Permalink to Comment

33. Anonymous on November 25, 2012 6:30 PM writes...

interesting, Pierre seems to be the only person who has read the 'Help' pages of CD seriously! Most of it are listed under Help/Contents/Shortcuts and Hotkeys on CD

Permalink to Comment


Remember Me?


Email this entry to:

Your email address:

Message (optional):

The Last Post
The GSK Layoffs Continue, By Proxy
The Move is Nigh
Another Alzheimer's IPO
Cutbacks at C&E News
Sanofi Pays to Get Back Into Oncology
An Irresponsible Statement About Curing Cancer
Oliver Sacks on Turning Back to Chemistry