ChemDraw 17: Faster editing, new features, still works with Word

ChemDraw 17 Review Part 1: New features

Test platform: ChemDraw Professional 17 (17.0.0.206), iMac 2011 8GB RAM, MacOS 10.12.6 Sierra; Microsoft Office 2011, 2016; and the latest Apple Pages 6.3, Keynote 7.3.

[Update 4 October: Added a short Youtube video showing the Drawing and Reaction Hotkeys in action]

I’ve spent about a week with the new version of ChemDraw now and have to say that this is probably for me the biggest feature leap for the product since Scifinder integration. My test machine is a comparatively old kit and it has run perfectly well. I should point out again, as I have noted before, that when these new ChemDraw versions come out, they are checked and certified for compatibility with the latest, shipping version of the Windows and Mac operating systems. On Mac, this means Sierra, as High Sierra was only released last week. Whilst I can’t foresee any reason why ChemDraw 17 wouldn’t run under High Sierra, it is not supported at this time. I normally expect formal certification for new OS’s in a *.0.1, *.1 or *.2 release.

The headline features of the new version of ChemDraw are new enhanced Hotkeys, HELM support, Document Tagging (metadata), and compatibility with the latest 64 bit Windows systems. But of course you all want to know one thing: Does it support round-trip editing with Word? In a word – Yes (but more on that later). This short review just covers the new features in the ChemDraw Professional application, which forms just a part of the ChemOffice Suite. As with previous versions which I have covered before, various packages are available for Macintosh and Windows PCs at different price points and features lists. The list of versions at the PerkinElmer SciStore is to be found here.

Hotkeys

The feature that I’m most excited by are the new enhanced Hotkeys. The first thing you’re going to want to do is take a look at the ways Hot Keys have been improved to make drawing of molecules much, much faster. Helpfully, Perkin-Elmer have provided a handy cheat sheet. It’s available under File -> Open Samples-Enhanced Hot Keys Cheat Sheet.

CD17CheatSheet

The Hotkey cheat sheet provided with ChemDraw 17

These enhanced shortcuts will, with practice make drawing structures so much faster. I recommend printing that Cheat Sheet out, laminating it and sticking it to the top of your monitor or pinning it above your desk. Take some time to learn the most common ones such as “3” for a benzene ring and “6” for cyclohexyl. If a significant chunk of your life is spent drawing and editing structures (think thesis writing!) then this will save your hands from repetitive back-and-forth mousing to click on template icons. PerkinElmer and Chemistry World are running a Webinar on the new ChemDraw 17 on October 24th at 4pm (UK time), so I’d check that out if you want to see this in action.

Actually, while you’re looking at that Samples menu take some time to look at some of the others that are included there. Most of these have been there before but they are worth reiterating as really useful starting points for many types of complicated figures. I particularly like the Grignard reaction summary slides made by Roman Valiulin (@RomanValiulin), and the GPCR pathway templates which you can use as a starting point for any signalling pathway you care to draw.

Grignard

Also new in ChemDraw 17 is a really neat new Reaction Hotkey feature. Lets say you have a simple 3 step synthesis with a core component. To generate a quick reaction scheme, simply select any object, hold down the command key and use an arrow key to automatically copy-paste a duplicate molecule in the direction you chose, including an arrow. So in the example below I drew the initial biphenyl, and then used “Command-Right Arrow” to create the first reaction, then  “Command-Down” and  “Command-Left” to generate the other two elements of the scheme. I then went back and using the hotkey “1” added a methyl group which was to become the changing element at the para position. The amino and iodo groups can be added without clicking and editing the newly created atom by simply using the “n” and “i” hotkeys respectively in mouse-over mode. The nitro group was the only thing that had to be edited manually.

Reaction Hot Key

HELM (Hierarchical Editing Language for Macromolecules) Support

What is HELM? Think of it as a kind of SMILES for biomolecules. Chemists use SMILES strings as a convenient way to move chemical structures from one format to another, or from database to database. Typically SMILES notation is used for small molecules although they can be used for larger biomolecules. The HELM project was started by scientists at Pfizer as a way of getting complicated biomolecules and their derivatives into a searchable form for corporate compound databases. The HELM project is trying to provide a way of systematically representing complicated biomolecules such as post-translationally modified proteins, peptide-DNA/RNA conjugates, glycosylated proteins, cyclic peptides and all of the above containing a range of synthetic and semi-synthetic amino acid monomers, and fluorescent tags.

Hexaleucine in HELM editor notation, HELM string, and expanded structure

Chemdraw now provides a way of creating and sharing HELM strings for these systems. If you’ve ever used ChemDraw’s peptide or DNA drawing tool (The BioPolymer Toolbar), the new HELM tool will feel familiar. The tool now provides tabs with which you can create the components of your molecule, lets say a short peptide sequence and a fluorescent tag as separate objects. In the sequence of pictures below below I have drawn hexaleucine, and an Alexafluor tag (Step 1), and then connected the objects using normal chemdraw bonding methods (Step2). Then using the Expand label tool (Step3) you can see the full molecule (Step4).

There are a few quirks in the HELM database currently. For example in the the CHEM tab of the HELM toolbar below, if you look closely you will see a few items that are named somewhat differently. For example the shortcut for adding an Alexafluor tag to a peptide has the abbreviation Alex and the mouseover name calls it Alexa Fluor 488 NHS ester, which as peptide chemists know is the reagent used to introduce an AlexaFluor tag (The N-hydroxysuccinimide ester), not the name of the tag itself. There are also somewhat confusingly two chem entities abbreviated chol.

HELM1

Step 1: Using the HELM toolbar to draw the components as separate objects

HELM2

Step2: Draw the bond between your desired positions

When you expand the abbreviations, ChemDraw also leaves a small label adjacent to each element (which I normally immediately delete)

HELM3

Step3: Using the Expand Label and Clean up tools.

HELM4

Step 4: The tagged peptide structure after clean up

Document tagging – User-defined metadata

Document tagging is a way of adding user-defined metadata to your ChemDraw documents, to enhance their searchability.  It is invoked in ChemDraw 17 from the Edit  -> Document Properties menu. If you have started from an empty document and not a corporate template then everything you see in the initial dialog is empty. There are no predefined fields so you can add items to the list pretty much as you want. I can imagine that in corporate settings there may be fields for user, compound identifiers, Project codes, company and division name etc. When you add a property, you can define it as being either optional, recommended, or compulsory to have the field filled.

Customisable metadata entry in Document Properties dialog

In academic settings this feature may be less rigorously adhered to as I can see that it would take a great deal of compliance. I can see the potential benefits though in chemistry groups where more than one person is working on a project. You could set project keywords, and you of course want to know who created the document in the first place. On their product page, Perkin Elmer note that these metadata are searchable by third party software including Attivio and Elastic. It will be interesting to see if they will also be searchable from within MacOS (Spotlight Search) or Windows Desktop Search.

Once again, PerkinElmer and Chemistry World are running a Webinar on the new ChemDraw 17 on October 24th at 4pm (UK time), during which they are sure to be showcasing these features live.

ChemDraw 2017 Review Part 2: Round-trip editing, a deeper look.

Whenever a new version of ChemDraw comes out the first question I get asked is always “Does it break round-trip editing with Word?” If I may steal for a moment a paragraph of my initial review of the 2016 release:

Much of this review is concerned with it’s interoperability with Microsoft Office 2011 (specifically Word), as probably the vast majority of theses and papers in (organic) chemistry written on Macs would be written with this or older versions of Word as leapfrogging software package upgrades have a long, and sometimes chequered history together on the Mac. For my previous posts on this subject see here, here, here, and here.

I am happy to report that this new version of ChemDraw does support round-trip editing with both Office 2011 and 2016 (as part of Office365). It behaves exactly as expected. Objects you’ve pasted in previously can be copy-pasted back into ChemDraw and edited, then pasted back into Word or Powerpoint.

Round Trip editing with Word 2016 and ChemDraw 17

Round trip editing with Powerpoint

Not such great news is that round-trip editing with Apple’s suite of Productivity apps, Pages and keynote  is still broken. It was broken during the beta cycle with an earlier version of Pages (v5.6.1) as well so it’s not just the High Sierra-ready versions that have broken something. It seems that unfortunately due to the way that objects get transferred to the clipboard in Pages/Keynote, those objects are not editable when they get pasted back into ChemDraw.

That’s the short version but for those who are interested, I dug a bit deeper and uncovered a few clues about what parts of the process do work.

Steps taken:

1) Open ChemDraw 17

2) Open ChemDraw file  “2NaphKKRaldehyde.cdx”

3) Select structure

4) Copy to Clipboard

5) Open Pages 6.3

6) Paste item

7) Save Pages document “CD17Pages6test.pages”

8) Quit Pages

9) Open “CD17Pages6test.pages”

10) Select the structure,

11) Copy to clipboard

12) Open ChemDraw 2017

13) Paste item into new empty ChemDraw17 document

14) Structure is not editable, see object with blue boundaries only

Once again, the blue bounding box means it’s no longer editable.

Interestingly however, the required vector graphic information is present in the Pages file, as evidenced by the fact that whilst within Pages if you right-click on the ChemDraw image you can choose the Edit Mask function:

Applying the Pages Edit Mask function

And you are then provided with the Pages Mask popup, which includes a resize by slider function. Somewhat weirdly when you drag the slider to increase the size the structure initially expands beyond the bounding box, but when  you finish, the popup disappears and you’re left with a truncated, but scaled up portion of the structure.

This truncated chemical structure was then pasted back into ChemDraw and unfortunately was still not editable, but did appear nicely scaled back in ChemDraw, and printed with no blurring of the lines.

Therefore it seems apparent that all the vector graphic information is present in the Pages document, but only some parts of it are transferring to the clipboard. Investigating further within ChemDraw 17, this newly pasted truncated structure behaves in some ways like a regular ChemDraw object. The initial structure above was created using the ACS template, but if you take the new truncated, but scaled up fragment back to ChemDraw and paste it in, it pastes at the scaled size. BUT, if you then use the “Apply Object Settings from…” function and choose a different template, in this case the RSC two-column format, it attempts a rescale, but gets it wrong. So there’s sufficient information placed back in the Mac clipboard from Pages that it knows it has scalable bonds, but can’t convert the information into an editable structure.

Advertisements

About martin

almost on holidays
This entry was posted in Chem, ChemDraw, mac, software, Uncategorized and tagged , , , . Bookmark the permalink.

6 Responses to ChemDraw 17: Faster editing, new features, still works with Word

  1. Wrt HELM, symbol names are unambiguous and can’t be reused. The two “chol” actually have longer symbols that are truncated in that view.

    Be careful removing the labels, doing so will prevent you from returning from the expanded to the condensed representation and also will likely prevent an accurate Copy As HELM operation.

    • martin says:

      Good to know. I’m used to deleting the labels from the old biopolymer toolbar to clean up schemes for presentations etc. Shall take care with HELMS then.

  2. More info on “Chol”

    The monomers in the HELM monomer toolbar have their symbols truncated to 4 characters. There is a tooltip to display the whole monomer symbol though. See https://pbs.twimg.com/media/DLQYAf8UQAA1cY8.jpg:large

    If you open the Monomer Viewer you can see the structure and see the whole symbol, see https://pbs.twimg.com/media/DLQYP03UIAEzTYV.jpg:large

  3. The other thing to be aware of with HELM is the inherent variability of the “dictionary”.

    With natural sequences, your “dictionary” is defined (AGTU etc for oligo’s, WTYP etc for peptides). Likewise for chemicals via SMILES or suchlike, your “dictionary” is defined and limited by the periodic table (C is always Carbon). HELM is specifically designed to be flexible for the end user to add their own items to the dictionary. However, this brings along challenges with curation and data integrity.

    We have worked closely with the HELM committee to both use their monomer dictionary and both correct it for errors, but also expand it where relevant. We strive to be aligned with their dictionary. However, anyone can define their own monomers, which is both fantastic (as that is WHY HELM exists) but also dangerous – what if i used the same symbol for something else, or a different symbol for the same thing. If you give someone a ChemDraw file it will transfer both the symbol and the underlying structure and help resolve should there be conflicts, but this isn’t the case if you just transfer HELM strings on their own.

    A core principle of HELM is that users can define their own monomers. Which is mutually exclusive to maintaining the control of monomers necessary for easy data integrity. As a capability it is powerful, but with power comes danger. we provide tools (conflict resolution etc) to help but some responsibility lies with the end user. At least until we have true canocalization tools and the ability to manage institutional monomer databases.

  4. Ned Jackson says:

    Round trip editing now appears dead! On my MacBook Pro, running High Sierra, with Chemdraw 17 (specifically 17.0.0.206 (131) shown in the “about” menu) and the MS word from Office 365 (version 16.8 (171210) in “about”) I don’t even get an image transferred when I copy and then paste into word. It looks like a SMILES string, but is too simple for the complexity of my graphics. With “paste special” I can force a graphic to be pasted, but it’s dead upon return to Chemdraw. Pasting into Powerpoint (same Office suite) appears the same as “paste special” to Word: it does deliver an image that can scale (I think it’s .pdf format) but is a dead graphic when I attempt to move it back into Chemdraw. Even old Word files where I used to be able to pull the image out and edit it now only give me a dead graphical block when I pick a chemdraw graphic out and pull it into the current version. Very frustrating. Since both tools have been updated in the last few months, I can’t say which to blame.

    • martin says:

      Bugger. Those aren’t the exact versions I have at the moment so I can’t check. Don’t you have a Time Machine Backup that you can roll back a bit and see whether you can retain functionality?

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s