Org Prep Daily

July 7, 2010

All your structure are belong to us

Filed under: Uncategorized — milkshake @ 7:02 pm

I downloaded Symyx Draw this morning, it is offered as a free program for academia. It is used for drawing reaction schemes, creating SMILES strings, entering structures into Symyx databases, etc. and I am quite anxious to get rid of it: Symyx Draw automatically assigned Chemdraw files to a default association with itself (all files, not just those accessed by/copied into Symyx Draw).  And now when I try to reset the file association back to Chemdraw with the help of Chemdraw file connection prompt my computer would ignore the change. A newly drawn Chemdraw file then comes out with a cheerful Symyx icon and will reopen with Symyx Draw too (unless I rightclick and select Chemdraw from the list)….  I do not wish to have all my Chemdraw files appropriated by Symyx Draw without myself deciding to do so. And its not like that they would have asked during the installation. And I resent that in this way they try to mess with a functionality of a (better) competing software that we have already purchased.

I have had some experience with this company: after Symyx acquired MDL, Symyx stopped offering standalone ACD access subscription. (Available Chemical Directory – the most complete database of commercially-available chemicals, their pricing and vendor contact info). Symyx wanted the MDL customers to switch to their Symyx Discovery Gate “all inclusive” chemical search package which also bundled ACD access in it. The cost of the Discovery gate is so high that many academic institutions cannot afford it; for example my current employer does not have it. But I had the misfortune of struggling with the  Discovery Gate in my previous job – its  Java-heavy web-based interface provides the ACD search functionality too – but for me the most important difference was that a regular search that used to take one or two click per compound with the standalone ACD database from MDL was now taking about ten clicks per compound  in the Discovery Gate (with the extra download delays in between): now try to browse through few hundred compounds in the ACD database with this dog. A Symyx customer service representative informed me that they were not offering the standalone access anymore but I could put my concerns into writing (I wrote them an e-mail and I never received a reply to it).

Also, several times I spoke with our chem-informatics guy at the previous job, about our compound submission database – we used to have a simple one from MDL that worked perfectly well  – before it got integrated into a spiffy new Symyx database. And he too has been really frustrated with the Symyx chemical inventory and bio data integrated database that we were using thereafter for our compounds and biology data and chemical collections and high-throughput screening – all in one unwieldy mammoth database. He told me that he had to eventually get a third party software and write a new interface for us in chemistry just to help us with viewing and searching our compounds after we had entered them into the Symyx database (for which our employer paid hundreds of thousands USD). He said he felt hamstrung by having to work with this enormous and poorly designed package that someone high above in the management had chosen for us.

I suppose is always the same – a ginormous all-inclusive package that hardly does any of its basic functions well – and the company that does not care about the needs of the users and promotes its “complete solutions” to the management folks who actually decide about purchasing this stuff… I have the impression that when Symyx bought MDL it set out to max up the profits while riding on the popularity of MDL software; I think in the long run Symyx will drive away many MDL customers by these tactics and will not create too many new ones because eventually the word gets around. For example the ACD access is pretty important but in the end one can get a list of vendors and commercial availability/pricing info from alternative sources.


The individual Chemdraw licence complete with a decent manual costs about $170 for academia and private users (I bought one for myself last year when I needed to prepare my job presentations). I have no special love for CambridgeSoft but at least they never pulled a surprise like this on me and never told me to go and stuff myself with my concerns.


  1. Symyx *is* awful. Clicking embedded Symyx objects the wrong way in Word 2007 crashed it for me. So I switched to ACD’s Chemsketch, saved the drawings as PNGs and inserted them in to a nice LaTeX file.
    As for the uninstallation, have you tried Window’s system restore?

    Comment by Peter — July 7, 2010 @ 7:18 pm

    • I will ask a colleague, he has the admin privileges on our network.

      Comment by milkshake — July 7, 2010 @ 7:27 pm

  2. I’ve been using Marvinsketch. It’s the only thing I can find that’s free and runs on Macs, and it’s pretty good so far.

    Comment by psi*psi — July 7, 2010 @ 8:20 pm

  3. If I remember correctly, you need to run the installer again and select the uninstall option. Brilliant, isn’t it?

    Comment by trythis — July 8, 2010 @ 1:09 am

    • I have to ask the colleague who has the admin rights – as I needed him this morning when I downloaded Symyx Draw. We can’t install/remove stuff on our PCs here without the authorization, even a browser flash plugin, so it gets awkward sometimes.

      Comment by milkshake — July 8, 2010 @ 1:35 am

  4. When Available Chem Directory was no longer available I switched from Isis/Base to another programme. Then when I got a new PC I could not reinstall IsisBase (which had been free for academics) and could therefore not access my own (mini) compound library database (a *.db file created in Isis/Base).

    However one of the tech guys at Symxy coverted it to a *.sdf for me to reimport into another format at the drop of a hat, even when I had neither bought nor used their software. There were even some technical glitches which meant the standrad export function did not work and manual intervention was needed.

    So whatever their product is like I found their (UK) tech support excellent compared to other such companies I have dealt with.

    Comment by anon — July 8, 2010 @ 8:35 am

  5. You can likely use the very simple solution to reassociate the CDX file opening with ChemDraw by using File Type Associations from Windows and reset the default. I’ve had to deal with issues like this when I managed ChemSketch and we did the same thing…making ChemSketch the default for opening ChemDraw files but when people want to switch back it wasn’t difficult. I doubt that Symyx are making it difficult on purpose. I’ve collaborated with them and worked with them over the years and they are very helpful. If you want the name of someone who can help you directly to solve the issue in a few seconds probably let me know offline (antonyDOTwilliamsATchemspiderDOTcom.)

    Comment by ChemSpiderman — July 8, 2010 @ 9:10 am

    • Thank you – this is helpful contact. Maybe it was a glitch somewhere, anyway it is gone for good now.

      I believe it would be much better for any new software to have an opt-in window popping up – or perhaps an non-obtrusive button on the bar (which would offer associating the cdx files by default) rather than doing this automatically and having the users to find the way to opt out: most people have Chemdraw and had spent considerable amount of time on their old presentations and sometimes recycle the old files into their new presentations: They have all these beautiful fonts and drawing settings selected to look good on the slides. So it makes a nuisance (and bad impression) if another program suddenly forces itself in.

      I believe the future is in the freeware (after all, the drawing programs are like text editors, they have been around for a long time) though I do not like Symyx Draw. I suppose they would want to control the database market and the Symyx Draw freeware is meant to be the foot in the door – so I am very suspect of anything that suddenly creates problems with using Chemdraw.

      Google for example is very good at the freeware tactics – they seem to take a great care of not annoying their users.

      Comment by milkshake — July 8, 2010 @ 9:54 am

  6. I ran into this very same problem- the constant annoying reminder that Symyx Draw was now the default editor for all chemdraw files. I was able to “almost” fix it in this way, following instructions at the Symyx web site:

    1. Go to Control Panel > Add or remove Programs and select Symyx Draw 3.2 EE – click “Change”.
    2. Click “Next” at the initial screen, and select “Modify” option at the Program Maintenance.
    3. Select “Developer user” if you want to have developer tools included. Click “Next”.
    4. At File Associations: “Do you want to associate CDX files and ChemDraw objects in MS Office application with Symyx Draw?” Default is Yes. You MUST select No, to associate CDX files to ChemDraw.
    5. Then proceed the installation. It will change the CDX file association to ChemDraw.
    6. reboot (they don’t tell you this)

    Now every time I open chemdraw I DO NOT get the annoying message about chemdraw not being the default editor. If I embed a chemdraw file into a new word or powerpoint document and then I later double-click on it, the image DOES open in chemdraw.

    The one drawback remaining, however, are the word files and powerpoint files that I created before making this change in the setup. When I open one of those files and double-click on a structure, SymyxDraw opens. Apparently that is because the association was not “fixed” back when I created that document. The only way to fix that, I suppose, is to copy the image to clipboard, delete it, paste it into chemdraw, then copy and re-paste it back into word or powerpoint. Annoying as hell. Moving forward, though, I should not have that issue, if the Symyx people are right.

    Comment by partial agonist — July 8, 2010 @ 11:30 am

  7. During the installation procedure, uncheck the associate ChemDraw files with Symyx Draw option and the issue should go away. ChemDraw handles its files and Symyx Draw handles its file. Simple really.

    Comment by kttaylor — July 15, 2010 @ 5:26 am

  8. There’s nothing better than Chemdraw. If you can, stick with Chemdraw 11, since there is nothing new in Chemdraw 12, except the version number.

    We’re also living through the last days of conventional Scifinder. They’re switching to web-based, which is actually not too bad.

    Comment by LiqC — July 15, 2010 @ 6:58 am

    • Chemdraw 11 is not supporting M office 2007…

      Comment by monk — August 8, 2010 @ 10:18 pm

  9. I recently purchased ICM-Chemist I think it is a good cheap alternative and most importantly gets the job done.

    Comment by POhare — August 8, 2010 @ 11:37 am

  10. The new web-based SciFinder is sooo damned slow! The old software (which I came to quite like over time) was never any race winner, but the new web interface is glacial. When I need to track down a dozen or two refs quickly, I don’t want to be stuck waiting for it to load!!!

    BTW: You can change the .CDX file associations by right clicking a file, select “Open With…”,
    then select ChemDraw from the list and check the box at the bottom that says “Always use this program to open .CDX files” … Done!

    Comment by Ryan K. — September 16, 2010 @ 8:29 pm

    • I did that and it worked for ChemDraw – but when copying and pasting structures and reaction schemes from ChemDraw to a Word document, the file automatically reverted again to to Symyx even though I had the file association right. In the end, uninstall solved all my troubles.

      PS: Completely agree about the web-based SciFinder. I think they still offer the non-web based version though, we have it here at the institute.

      Comment by milkshake — September 17, 2010 @ 10:00 am

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