Sunday, July 20, 2014

Review: ChemBioDraw 14.0

Dear ChemBioDraw* Ultra 13.0,

Listen, we had a good run together. But I've fallen for another: ChemBioDraw Ultra 14.

My good friends at PerkinElmer (PKI) were kind enough to grant me trial access to their spiffy new chemistry drawing software. As an avid user since, oh, say, ChemDraw Pro 4.5, I feel confident in stating that this version wins all around for smoother operation, better templates, easier file export, and better shortcut keys.

So, I figured what PKI really wanted me to do most was to try and BREAK ChemBioDraw 14.0
 . . .if I could. Did I succeed? Let's talk a walk through the software and find out.

CBD 14.0 means NEVER seeing this screen again (hooray!)
Starting at the top, I figured I'd check the "What's New?" link in the help menu. One thing I appreciated more than I thought? ChemBioDraw 14.0 directing "Help" queries into the appropriate section of the User Guide. Version 13 still spawned its help window inside Windows help, with the infamous purple booklets leading you down wild goose chases of clunkily-presented information.

Drawing hasn't changed much since 13.0. At least the text direction auto-correct -- which drove me batty in former iterations -- seems to have been tweaked; the system now opens my older drawings the way I typed 'em in originally (hence, below, attaching pasta sauce to a scaffold in place of a sugary placeholder).

I promise this made sense in earlier ChemDraw versions...

The CBD 14.0-to-SciFinder jump works much more smoothly than I had anticipated. For those of us who shuddered through dial-up desktop versions of SciFinder in the late '90s, this version feels like the sleek Lamborghini of the search world. After drawing (or importing) my structures of choice, I lassoed them up and pressed the little "SciFinder diamond" on the top toolbar. Within about 5 seconds, a new window opened with the standard exact / substructure motif. Two clicks later, I'd be deep into the primary literature.

So, my goal was to break the system, right? Here's a logical place to try - I attempted to load each and every complex structure I had drawn since starting my fledgling blogger's career, around 2009 or thereabouts. Again, I was amazed by the speed and accuracy of the SciFinder pop-out, which returned roughly 90% of the correct molecules I'd searched for (below):

From this 2011 post
From this 2013 post
From this 2014 post
However, it's not all bubbles and sunshine. Two of my molecular queries bore no fruit**; perhaps they're too new to have been uploaded into CAS's databases yet. But one thing remains tricky: drawing and searching for metallocenes. Along with their new push into biology clip art, ChemBioDraw has a renewed focus on making sure you've got those sandwich compounds properly aligned.

Sigh. If only I remembered what they were all supposed to be...


Now, even after aligning my query using the proper template, SciFinder makes a mess out of it.

From this 2012 post

So, obviously I went looking for things to break, and found some rather limited examples. Honestly? The rest of the program works pretty well. And writing this review gave me a wonderful opportunity to poke and prod at the product in ways I hadn't in far too long.*** I finally realized you could change the solvent on the NMR predictor! I played around with expanding and collapsing peptide and RNA strings. And the post-drawing mods to more complex peptides, like disulfide and lactam cross-linking? Much better.

Found on p. 126 of the User Guide. (Get it?)
I'd like to shake the hand of the person who slipped this in...
R.I.P., Optimizing Octopus

I will take this final moment to remember a long-lost piece of ChemDraw lore. Once upon a time, to "clean up" one's structures, the icon looked something like this (right). I've heard it referred to as a jellyfish, a squid, a broom (no!), but I always knew it as a friendly little octopus. With CBD 14, any doubt about its brushiness has been cast aside with a full-out icon redesign.


Looks great, guys. Now let me think about more ways to use it for actual work!

Thanks again to Philip Skinner and PerkinElmer for the chance to review the software.
---
*For other blog reviews of ChemDraw products, see Jess The Chemist, Andre the Chemist (no relation), or Chemjobber.

**Here's the structures that returned empty SciFinder searches. Both compounds (left, right) were first reported in 2014.



***P.S. I never knew you openly solicited beta testers for these products...gimme a call sometime, PKI!

6 comments:

  1. What Perkin Elmer still failed to include: A way to make life a little easier for the thousands of undergraduate and graduate students that are forced to write their theses in MS Word and therefore will have to carry out numbering of all the embedded chemical structures manually.

    There is a way to this in Latex where you can place a variable in a postscript file and directly let Latex change your numbering when the order of appearance changes.

    The fact that Perkin Elmer still fails to come up with this very basic but extremely important feature for MS Words shows their blatant disrespect for a large percentage of their non-industry users. Those of course, will usually not pay that much into Perkin-Elmers money pot, but that institutions that host them will.

    ReplyDelete
  2. Did they fix the Ctrl+Shift+Alt+H R/S flipping issue? cf: https://twitter.com/azmanam/status/251693307430838272

    ReplyDelete
  3. @azmanam - I will try to check for you and report back. If you want to test yourself though you can download a free trial of v14 here http://bit.ly/1p7yhJU if you don't have access already.

    Young Padwan - Thanks for the suggestion. The software only improves on the basis of suggestions from the user community. We are aware of this desire but it would help to add more voices to this request. So, please could you report this though our support channel, which can be used for feature enhancement requests also. You can submit those requests here: http://bit.ly/1o0lqtL

    ReplyDelete
  4. And @SeeArrOh - thank you for such a comprehensive review, we really appreciate it. There really is no substitute for people trying our software in real world uses. This wasn't a beta test per se, as the software was already released, but we do do those on a lot of our software, especially add-ins for the Tibco Spotfire platform and a new web based ELN/scientific collaboration platform (Elements) we have been developing http://bit.ly/1sF5SOX

    ReplyDelete
  5. "I finally realized you could change the solvent on the NMR predictor!" And the field strength too. Not that I wanted to return to my postgrad days running lanthanide complexes on a 60MHz machine.

    ReplyDelete
  6. Still just DMSO or chloroform? You've had those options for a while :)

    I laughed out loud at your 'ragus'. I'm still laughing now. I have no idea why I find it so funny :')

    ReplyDelete