[Update March 1. ChemDraw 16.0.1, ChemDraw 16.0.1 press release principally addressing stability and usability issues on the Mac platform has been released.]
A quick update on my earlier post. I have managed to get ChemDraw 16 running on MacOS 10.12.1 Sierra. I installed Sierra on an external USB self powered hard disk, so performance is a bit slow but the important details are as follows:
I have not tested all functionality of ChemDraw 16 under Sierra for the moment. But for me, the most important question, “Does round trip editing work with Word 2011, PowerPoint 2011 under Sierra?” can be answered with a big “YES”. Here is a pic of a structure from the previous post pasted back into ChemDraw 16 from Word. The structure is editable, and can be transferred back to Word (or PPT). But please note, this is not supported yet by CambridgeSoft. Officially Sierra is not supported. It’s just that the features I have tested on one machine work.
On this Sierra boot disk I have now also updated the copies of Pages, Keynote and Numbers to their Sierra release versions however disappointingly Round Trip Editing (RTE) still does not work on my test platform. So to summarise, neither the El Capitan versions of Pages (v 5.6.2) or Keynote (v 6.6.2) or their Sierra release versions, Pages 6.0.5 or Keynote 7.0.5 support RTE. Office 2011 does.
P.S. I have not tested RTE on OpenOffice of any flavour as I have a thing about Java. Also if anyone else has read this far, pasting ChemDraw structures into a Google Doc does not work. Docs doesn’t recognise the clipboard contents. You can do it by inserting a graphic (PNG etc) sure, but the editable features that make a ChemDraw structure work aren’t incorporated, so why would you even?
[Update March 1. ChemDraw 16.0.1, ChemDraw 16.0.1 press release principally addressing stability and usability issues on the Mac platform has been released.]
[Update Dec 26. ChemDraw 16 is now internally approved to run under MacOS Sierra. Please read this post in conjunction with my brief Sierra update]
I got my hands on the shipping version of ChemDraw 16 last week and so have been busily assembling factoids and tweeting a bit about it over at @MartinStoermer
First things first. My test platform is a 2011 27” iMac with 8 GB RAM, Running MacOS 10.11.6 (El Capitan), and Microsoft Office 2011 (14.6.8). The release of ChemDraw Professional that I am reviewing is version 184.108.40.206. So up front I will say that this is not a review of ChemDraw 16 running MacOS Sierra. I hope to study ChemDraw under Sierra in a later post, but as of the time of posting Sierra is not a supported platform according to Cambridgesoft.
[Update Monday 14th: I made a Sierra boot disk and ChemDraw 16 runs. Not sure about all functionality but round trip editing WORKED with Word 2011, PowerPoint 2011, ChemDraw 16.]
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. But first let us go through a few of the new features.
Versioning is a feature most Mac users will be familiar with, but now happily ChemDraw fully utilises versioning on the Mac so that all saved versions of a file are accessible from within that file via the “File – Revert to… – Browse All Versions” menu. If you have not used this feature before this is what it looks like. A flip-through interface where you can step back to previous versions of a Document.
This does not mean that users can get lazy however, I still recommend doing the odd “Save As…” to keep what are now redundant copies. Autosave simply means that items left open and unsaved when you quit the app will reopen when the app is run again. Incidentally, “Save as…” is now a hidden menu item in recent Mac OS’s, a “feature” I find a bit annoying. But it is easily accessed by holding down the Option key while using the File menu.
According to the release, multi-monitor and Retina display support is improved. I don’t have a high res monitor and haven’t tested multi-monitor systems yet.
When gleefully tweeting that I had gotten hold of the new software I immediately tweeted that ChemDraw now had emoji enabled, so yes, you can use a Dog as an atom label or in any text box really. This is because behind the scenes, ChemDraw now supports Unicode, the underlying technology that runs emoji, among other things.
Cats of course are not excluded, and mice, which in this #ChemNobel year lead to some appalling puns.
And this Rodentaxane:
But the main thing we are interested here is not the new features but rather how does the new version fare with round trip editing. One of the reasons I am running a 5-year old version of Office is that the history of round trip editing is somewhat disappointing. In Ye Olde Days once you had pasted a ChemDraw picture or Scheme into a Word document, you could subsequently edit the structure by double-clicking it and ChemDraw would be launched. You could make your changes and then save it, and be returned to Word with the amended scheme in place. The technology used here was OLE (Object Linking and Embedding) developed by Microsoft. Microsoft dropped OLE support in 1996 in favour of their ActiveX controls. This never worked on the Mac version of ChemDraw due to changes in the OS but did work in the Windows version. Mac users had to copy the picture to the clipboard in Word, and paste it into an empty ChemDraw window and edit it. Then they had to copy the new structure or Scheme in ChemDraw and return to Word, and paste the amended scheme in. If anything went wrong, you ended up with an uneditable blue bounded box
This process of round trip editing and has proven to be problematic nearly every time a new version of either Word, ChemDraw, or MacOS comes out. The nature of the way ChemDraw structures were copied to the clipboard also changed along the way. The format changed to an enhanced PDF that contained both a bitmap version, and the underlying vector information (in CDXML) that described the structure. So why does this continue to be a problem?
Firstly it is important to know that when a new version of ChemDraw is in development, CambridgeSoft write it to be compatible with the current RELEASE version of the operating system, not the version currently in beta testing. The same with Word/Office compatibility. Development versions of ChemDraw are tested with the current release versions of Office and one or two versions back. Thus this iteration of ChemDraw is not explicitly supported under Sierra. I strongly recommend users NOT to upgrade to Sierra if you plan on using this or other versions of ChemDraw. I am in the process of setting myself up a Sierra boot disk to see whether and where it breaks. My suspicion is that it won’t, just that some Sierra features may not work. So stay tuned for an update to this post
Based on years of experience I am always loathe to update my Mac Operating system or Office version without first knowing that everything will work together. So currently I am using Office 2011 and the new ChemDraw 16 on my home computer (running El Capitan). Our IT department at work is also conservative with updates. The default system configuration for users in our group is an El Capitan Mac, with Office 2011 and ChemDraw Professional 15. And we can do the round trip editing just fine.
So the biggest question for us at least is “Does ChemDraw 16 do round trip editing with Word 2011?”. And the answer is Yes! I did my standard test and am happy to report that I had no issues.
But wait you say, Not everyone uses Word 2011. Some people use 2016, or even Office365. Some people use one of the various OpenOffice trees. I don’t have any of those to test currently. I’m certainly not about to go out and buy a new Word. Most of my actual writing these days is done in Scrivener and I only use a late-stage export to RTF if I need to conform to some template. But the release material suggests that the last two versions of MacOS (Yosemite and El Capitan) are supported, as are Microsoft Office 2011, 2016 and 365. So I expect that round trip editing will work just fine with them too.
Incidentally, the above procedure also works for Powerpoint and Excel 2011 editions:
However for some of my writing, and I know several colleagues do too, I use Pages and Keynote instead of Word and Powerpoint. Sadly for me, a ChemDraw object pasted back into ChemDraw via Pages (v 5.6.2) or Keynote (v 6.6.2) was no longer editable. You get the familiar bitmap image with a blue bounding box, but it is not editable, beyond simple resizing. I have had reports that this does work for some users but I have not been able to reproduce this on my test system. I may install the new ChemDraw on my work laptop and see if a different machine might do it, if there is some weird machine-specific bug but I can’t do that just yet.
In all other features that I’ve looked at, ChemDraw 16 looks and behaves a lot like the previous versions. Everything is pretty much in it’s familiar place, except minor changes to the Scifinder Link button, and a new icon to go to ChemDraw Cloud. ChemDraw Cloud is a whole new web application that I hope to review at a later date.
ChemDraw is available in several versions in addition to the Professional version I’ve reviewed. Rather than go through each in turn I suggest you go to the official product pages (here) which gives you the brief outlines. Remember that The Full ChemOffice Suite with ChemDraw E-notebook, Chem3D is a Windows only product.
Importantly, the symposium is being promoted by the Royal Australian Chemical Institute, which previously had been partially semi in-charge of BBOCS. I have mixed emotions about this change. Let me explain.
(Full disclosure: I was on the organising committee for BBOCS when our group at IMB hosted in 2001 and 2007. )
BBOCS evolved from the old Organic-only BOCS symposia and I can see the reasons for making it a bigger conference style day where there are multiple concurrent sessions. BBOCS was always a bit of an ad-hoc affair with a rough rotation system of the three main universities in SE Queensland rotating hosting duties among the various chemistry departments and the research institutes. Let’s just say that in some years there was less input asked for or given by the RACI and some organising committees did their own thing in terms of arranging the remainder of the program, whether there would be poster sessions or not, whether alcohol would be served afterwards or not, and what prices would be charged. In years when the RACI was heavily involved, a strict tiered pricing structure required centrally by the RACI was used. Typically there would be Member and non-member pricing at around the $45/$65 mark for non-students, and $20/$30 for students. There were also restrictions placed on how sponsors were sought, and how sponsors dollars went into RACI bank accounts and were dispersed when required. Often, when the research Institutes hosted the event we charged a lower flat rate for entry, went after more sponsor dollars to cover the difference, and used our own banking arrangements to collect registration fees. This lead to some disquiet within the RACI and on one occasion a snarky one-liner in an issue of the RACI magazine, Chemistry in Australia, that a summary of the symposium could not be provided in the annual report along the lines of “The RACI had no involvement in the running of the conference this year”. In some years, the organising of the event was a bit of a last-minute affair and in one case it was cancelled altogether. It is to be hoped that bringing all the disciplines together and formally running it as an RACI event may finally lead to a more permanent and settled format.
For many young and aspiring chemists, particularly honours students the local symposia were an ideal introduction to scientific conferences. They were small, they were short, and importantly gave students a glimpse into what other research was out there. Coming as it did towards the end of the calendar year, when most of the pressure on honours students was off it gave students a chance to shop around locally, out of their one-year bubble, for possible postgraduate research and potential supervisors. The invited, usually overseas plenary speakers also gave postgraduate students a chance to look a bit further afield, perhaps towards a future postdoctoral position
It is not yet clear who will be the plenary lecturers at this years symposium. BBOCS has had a troubled past in with invited speakers suffering from a very poor gender ratio. I have previously blogged on this subject so will not elaborate here. I encourage you to read that earlier piece but suffice it to say the local Brisbane organising committees had no say in the speakers provided nationally by the RACI, but selected by the Victorian branch of the Organic Chemistry division.But why merge the symposia at all? As recently as last year, the RACI held it’s own medicinal-chemistry one day conference, held a few months before, and almost certainly in competition with BBOCS, removing the incentive for people to go to a second biological chemistry conference a couple of months later.
Why has the strategy now changed to running a combined event? Perhaps there are costs to be shared by holding all the local events together in one go. There is no denying that funds are tight in many chemistry departments, but I see a major problem in going down this path. If this is to be an annual event, will it not be in major competition to the RACI national conferences, especially next year in the RACI’s centenary when a major conference is being held in Melbourne in July (2017).* Will cash-strapped research groups be able to justify sending their students and postdocs to two generalist conferences in Australia in one year, in addition to funding travel to any overseas conferences?
It remains to be seen whether this new event, supplanting the sometimes chaotic, but well-loved and attended BBOCS is well received. A good start would be to get the invited speaker list out NOW, and make sure it has a better diversity profile than in the past, including the RACI’s own medchem conference Brisbane last year which had no women plenary lecturers. An a clear statement on the conference website (there isn’t one at present) detailing their diversity policy would be a good step too. As always, please send me suggestions either here, if the comments are working, or on Twitter @MartinStoermer.
*Previous version of this post incorrectly said Adelaide. Whoops.
So here’s the thing. A few people have been tweeting sciencey-looking articles into my timeline of late, which come from the website scienmag.com which bills itself as Science Magazine, and the Twitter account of the same name, @scienmag with the name Science.
I recently stopped following this account for a number of reasons, chief amongst them being that they are clearly trading off the name of the well-respected scientific journal/magazine Science. The latter, published by the AAAS famously uses the web address http://www.sciencemag.org and the Twitter handle @sciencemagazine, as in the early days of the commercial internet for one reason or another, science.com was already taken, and similarly, in the early days of Twitter @science was quickly snapped up.
Now most scientists I know do not get the two confused, but every now and then, even quite prominent scientists forget and RT articles from Scienmag. In fact when I started on Twitter one of the accounts I started to follow was @scienmag, thinking it was the real deal. I soon learnt it wasn’t but was too lazy to unfollow them.
But the main reason that I dislike @scienmag, and the final prompt for me to unfollow is that it seems to take science stories from various sources, often press releases about new research, and publishes them verbatim or near enough on their website, but annoyingly nearly never provides the link to the actual research article in question.
Why would they do this? Well it all comes down to the commercial web page principle of eyeball residence time. Basically websites that make their money selling advertising space never want you to leave their site by anything but a sponsored ad (usually Google ads). In fact, the only links off the page you may have arrived at are ones going to other Scienmag stories, or ads. What we as scientists want to do of course is get to the actual science as fast as possible, so we would likely just click on the actual journal link and leave their webpage behind. Thus creating a very low eyeball residence time, and therefore less ad dollars for them.
Take this example that crossed my Twitter timeline this evening. It was a retweet of a quote tweet that linked to a Scienmag page about survivors of pediatric Hodgkin lymphoma studied at St. Jude Children’s Research Hospital and their long-term disease burden.
And as you can see it looks like an original magazine article, complete with quoted scientists that you might be led to believe were actually interviewed by the journalist. But there is no link to the Lancet Oncology article under discussion.
So I went to the St Judes web page and looked around for their press release on this subject and found this, that is strikingly similar to the “story” at Scienmag:
Except that this time, there actually is a link to the real published article at Lancet Oncology.
One of my major research interests is the Flavivirus group of viruses. In our work at the University of Queensland we’ve been involved in developing inhibitors of viral proteins associate with Dengue and West Nile viruses. Particularly inhibitors of the NS2B/NS3 protease and the surface E-protein [1,2,3]. A key way to target these proteins is to examine their X-ray crystal structures. A newer technique of determining the structure of proteins is cryo electron microscopy (Cryo-EM).
I found myself on Thursday looking at the Cryo-EM structure of the entire Zika virus, published recently by the Kuhn group . Zika is in that same class of Flaviviruses and is therefore of great interest to me not only because of the recent flurry of media commentary and public health concern surrounding current outbreaks. The Kuhn group had previously published Cryo-EM structures of the Dengue and West Nile viruses as well.
I wanted to take a closer look at the structure so I used my favourite visualisation program Pymol to take a look. After a bit of fiddling, which I’ll go into below, I got to this lovely picture of all the surface proteins of a Zika virus particle, with all the chains rendered as cartoon helices and sheets etc.
I was quite please with the result and posted it to Twitter. I next made a Quicktime movie direct from Pymol of the whole picture spinning 360° over 4 seconds, and posted it to YouTube. The result is a bit pixelated because I just used the default YouTube compression settings which reduced the 28MB Quicktime file to an 808KB Youtube video.
A few kind people commented on the structure which has a lovely symmetry to it but my interest was piqued by one Twitter user Jonas Boström (@DrBostrom) who was interested in whether I’d be happy to share the viral assembly as a single PDB file so he could look into making a VR version. Sure I said, and went back to Pymol and first myself tried to save it as a PDB and VRML2 file, which is one of Pymol’s export features. Some time later I had a 54MB PDB file and a, wait for it, 2.93GB .wrl file. Not really the size of files you want to pop into a tweet! Even when I gzipped the PDB file it was 12MB. But there was a problem. Before I go into the problems and the techniques required in Pymol to get the assembly just so, I need to fill you in on a little of the background to these surface proteins.
The surface proteins of the viral particles are a mixture of the E and M proteins arranged in a regular pattern; 360 proteins are arranged in an icosahedral shell. If you go to the PDB page for this structure and download the PDB file 5ire.pdb what you are getting is the asymmetric unit which consists of just 6 chains A-F. Three repeats of the E-protein (A-C), and three of the M protein (D-F). There are 60 of these subunits in the Biological assembly giving the total of 360 total viral proteins at the surface 180 E, 180 M.
So lets just take a look at this subunit for a bit. This smaller more manageable chunk of the overall virus surface is the best one to use if all you are interested in is the way these proteins interact with each other, or if you’re interested in the important Asn154 glycosylation site (boxed in the figure, one glycan for each of the E-protein chains).
But if you want to visualise the whole viral surface proteins you want to download the “biological assembly” file, which when unzipped runs to 54MB.
If you decompress and then open this file in Pymol, you will see at first just the one subunit, as above, but note that it has been loaded as 60 states (boxed in the figure). You can cycle through these with the play button but we want to visualise them all at once. To do this we use the split_states command at the Pymol command line. This splits the multi-state file into 60 new objects. In this case I have given each new object the Zika prefix. You can now delete the original multistate object for neatness. You will probably need to click the zoom button to get them all into the window (or type zoom at the command line).
split_state 5ire_assembly, prefix = zika
Now we can see all the subunits all at once and things start to get a bit more tricky. If you have a reasonably modern Mac or PC you should be fine unless you try and make some fancy surfaces, in which case you might find your machine chugging a bit. But for now the first thing you should do is save the session as whatever file name you want in case the next few steps cause Pymol to crash. Pymol adds a fair bit of overhead to these session files so you’ll end up with something about 210MB in size.
You might want to experiment with turning the cartoon representation on too at this point. This is also the point at which I made that short spinning video I mentioned earlier. The next thing you will probably want to do is save the resulting assembly as a single PDB file so you don’t have to repeat this process, or perhaps you want to offload the file to a different modelling package, like Jonas Boström suggested via Twitter.
Fortunately Pymol lets you export/save multiple objects into a single PDB file. The simplest way to do this is via the “select” function. At the Pymol command line type:
Everything should now be highlighted. Now choose File-> Save Molecule and in the dialog box scroll down and chose “sele” as the object to be saved, then give it a file name, and wait…
In our case the resulting file is about 54 MB but there is a big problem. To demonstrate, open the PDB file in a text editor and scroll down. I used Smultron and you have to wait a fair bit as it’s going to get very laggy. Anyway if you scroll down far enough you will discover a problem I had not encountered before. Pymol doesn’t seem to be able to export a PDB file more than 99999 atoms long properly. This file contains over 660000 atoms, and every one past 99999 is numbered 99999.
This as you would expect is going to cause problems, not least when we get to the CONECT records part of the PDB file. Behold the ugliness. However, all the xyz coordinates are legit. Let’s see what happens when we load this big PDB file back into a new Pymol session. Whoops, see all those extra long bonds? That’s trouble.
Fortunately CONECT records are not completely necessary in a PDB file if you just want to do simple visualisations. So in a text editor it is a simple matter to remove them all. The resulting edited PDB file can then be read back into Pymol without all those nasty extra lines, but…
…there’s a new problem. This export-import routine introduces some weird forgetfulness about what secondary structural elements the protein contains. So Pymol does nothing when you try and show a cartoon representation of the proteins. The normal thing to do in these circumstances is to run the util.ss from the Pymol command line. I did this and got the famous Apple spinning beachball of death. I stuck it out however (put the cursor in the “do not sleep” corner and went and made coffee) and eventually Pymol came back to life. But it was a long wait (20 minutes). This is a pretty good place to point out that this was all done in Pymol 1.6 on a 2011 iMac (2.7GHz, Intel Core i5) running 10.10.5 with 8GB RAM. But the process eventually ended up a failure. Despite showing all the right messages in the log box, no secondary structural features could be obtained.
util.ss: initiating secondary structure assignment on 103680 residues.
util.ss: extracting sequence and relationships…
util.ss: analyzing phi/psi angles (slow)…
util.ss: finding hydrogen bonds…
util.ss: verifying beta sheets…
util.ss: assignment complete.
Save: Please wait — writing session file…
So the process is not yet complete. But the good news is that I have a PDB file that doesn’t make wonky bonds. The bad news is that I still have >500000 atoms with atomID 99999. Clearly this job is a bit beyond Pymol’s current abilities. I shall keep you posted. Once I have some more functional files I may put them in a public Dropbox if anyone wants them, as they’re still a bit too large to email.
 “Potent Cationic Inhibitors of West Nile Virus NS2B/NS3 Protease With Serum Stability, Cell Permeability and Antiviral Activity.” Martin J. Stoermer, Keith J. Chappell, Susann Liebscher, Christina M. Jensen, Chun H. Gan, Praveer K. Gupta, Wei-Jun Xu, Paul R. Young, and David P. Fairlie, J. Med. Chem. 2008, 51(18), 5714-5721. Full text via ACS publications
 “Structure of West Nile Virus NS3 Protease: Ligand Stabilization of Catalytic Conformation.” Gautier Robin, Keith Chappell, Martin J. Stoermer, Shu-Hong Hu, Paul R. Young, David P. Fairlie, Jennifer L Martin J. Mol. Biol. 2009, 385(5), 1568-1577. Full text via ScienceDirect.
 “In silico screening of small molecule libraries using the dengue virus envelope E protein has identified compounds with antiviral activity against multiple flaviviruses” Thorsten Kampmann, Ragothaman Yennamalli, Phillipa Campbell, Martin J. Stoermer, David P. Fairlie, Bostjan Kobe, Paul R. Young Antiviral Research, 2009, 84(3), 234-41. Full text via ScienceDirect.
 The 3.8 Å resolution cryo-EM structure of Zika virus.
Sirohi D, Chen Z, Sun L, Klose T, Pierson TC, Rossmann MG, Kuhn RJ.
Science, 2016, 352(6284), 467-70. Pubmed Link.
Opinions vary wildly on the internet indeed as elsewhere about who was the best James Bond. From die-hard Sean Connery fans to those who swoon over a buff Daniel Craig. Today I take a look at the Bond phenomenon. Not to arbitrarily comment on who was the best, but rather to focus on who was the hardest. And to help me I am turning to science. More specifically, the Moh hardness scale.
So by extracting chemical elements from their surnames we arrive at Sean Connery as Cobalt with a Moh hardness of 5.5. Next comes David (Nickel) Niven who is a bit softer with a Moh hardness of 4. George (Lanthanum) Lazenby is softer still at just 2.5. Roger (Molybdenum) Moore is unexpectedly hard at 5.5.
Timothy Dalton presents a bit of a challenge as there are no Da elements though the name itself is very apt in this context. However if we cheat just a little and skip one character we can call him Timothy (Aluminium) Dalton, which has a Moh hardness of 3.
Pierce Brosnan also requires us to cheat a bit as Bromine is a liquid and doesn’t get Moh hardness number (but is a well hard element in its pure form let me tell you!). So we’ll get a bit creative and call him Pierce (Bronze) Brosnan, which gives him a modest hardness of 3.
But the undisputed winner in this contest is the current Bond, Daniel (Chromium) Craig with a Moh hardness of 8.5
That’s pretty clear to me.
So in descending order:
|Bond Actor||Mohs Hardness|
|Daniel Craig||8.5 (Chromium)|
|Sean Connery||5.5 (Cobalt)|
|Roger Moore||5.5 (Molybdenum)|
|David Niven||4 (Nickel)|
|Timothy Dalton||3 (Aluminium)|
|Pierce Brosnan||3 (Bronze)|
|George Lazenby||2.5 (Lanthanum)|