Major upgrade to WebCSD – The small molecule crystal structure database

[Update 16th June: Added Note about Pymol 1.8.4]

The new version of WebCSD has arrived and with it, a few new important features, such as improved substructure searching, and advanced text searching. The Cambridge Crystallographic Data Centre (CCDC) houses the the Cambridge Structural Database (CSD), a repository of over over 875,000 small molecule structures from x-ray and neutron diffraction analyses.

Growth in the CSD. Graphic copyright The Cambridge Crystallographic Data Centre http://www.ccdc.cam.ac.uk. The Cambridge Structural Database, C. R. Groom, I. J. Bruno, M. P.
Lightfoot and S. C. Ward, Acta Cryst. (2016). B72, 171-179 DOI:
10.1107/S2052520616003954

Traditionally, use of the CSD has been by institutional licensing of the desktop client Conquest, and by downloading periodic updates. The current release is May 2017. Recently a Java/Web interface WebCSD has become available for use, which contains fewer features compared to Conquest, but which is useful for accessing structures if you are out of the office or working from home. Unfortunately, I frequently had problems with the previous version which used to throw up lots of erroneous Java errors on Mac, claiming that the user had an out-of-date Java version. Happily this annoying bug seems to have gone with the new version.

Java Error with WebCSD v1.1.2 on Mac

Another confusing thing about the old WebCSD was that it used a different login system from the CCDC data deposition interface, requiring crystallographers or IT departments to maintain separate logins. In the new version you log in with your data deposition username/password at the main CCDC home page. The first thing you will notice is that the new CCDC home page now has two large button options:
Deposit structures and Access Structures.

new CCDC home page

Choosing Access structures takes you to the new WebCSD text and structure search interfaces in a familiar tab format.

Text Query Interface in the new WebCSD

Substructure search in the new WebCSD

I first gave it a quick try in text mode looking for structures of my current favourite mushroom toxin cyclic peptide α-amanitin. The results page has all the structures preselected in a tickbox format and encouragingly there is a “Download Selected” button.

Hits Page in WebCSD

This may not seem like a big deal but one of my major gripes with previous versions of WebCSD was that it was not possible to do a bulk download of hits. For that you have to use the Conquest interface, something that is impractical to do off-site.

So finally you can download all the hits, but currently only as a multiCIF file. This is not the easiest option but better than nothing. I’m currently trying to find reliable ways to convert or read multiCIFs. Pymol loads them all but only puts bonds in for the first entry (see pictures below). Update: Newer versions of Pymol (I used 1.8.4) read in all the files in a multiCIF correctly.

MultiCIF files opened in Pymol (v.1.6). First entry shows bonds, later entries just show atoms.

New versions of Pymol (v.1.8.4). show all atoms and bonds correctly*

Schrödinger’s Maestro only reads only first of a multiCIF file. The CCDC’s own software Mercury reads them all into the viewer window, from which you can select and export the files in a variety of formats, but you still can’t bulk export them all to another format.

Amanitin hits from WebCSD displayed in Mercury

I next tried searching for a substructure, a cyclic octapeptide equivalent with four thiazoles. Excuse the drawing, I’m still coming to grips with the interface and rotating etc. This came up with one hit, which happens to be a symmetric compound with four prolines occupying the remaining four amino acid positions. (Link to paper)

Substructure search interface. Had trouble finding rotate or cleanup tools

Nicely, there is a JSmol rotating 3D model of the structure as well. This hit also shows how this class of modified peptide macrocycles frequently bind solvent molecules and metal ions, In this case I have caught the rotating JSmol at the right angle to see a nice molecule of acetonitrile bound in the centre of the macrocycle.

WebCSD substructure hit interface

This has been only a very short overview of the new version. Stay tuned for anything else I discover. In particular one of the best things about new version is that is much much faster. I look forward to the products continued evolution, particularly the ability to extract hits to SD files, which is a standard feature of the desktop version.

*I should note that multiCIF files often contain coordinates for disordered atoms and these may display weirdly in Pymol. Pymol uses distances to estimate bonds, so some downloaded structures may appear to have chemically unfeasible connectivities.

Posted in Chem, software, Uncategorized | Leave a comment

New initiative: The Molecular Sciences Software Institute (MolSSI), based at Virginia Tech. via @ACSPublications

“A new computational chemistry software institute, the first of its kind funded by the National Science Foundation, aims to bring software development in the field up to speed with rapid advances in computer hardware.

The Molecular Sciences Software Institute (MolSSI), based at Virginia Tech, celebrated its launch with a reception on Tuesday at the American Chemical Society national meeting in San Francisco.”

I haven’t had a good look at this yet, I just saw this over at the ACS Meetings page. This looks like a really interesting initiative from the NSF. I can’t see any current job openings on the site, the last round closed in November 2016 and the Fellowships in February 2017. Something to keep an eye out on for when the next round opens.

Posted in Chem, software, Uncategorized | Leave a comment

ChemDraw, Chem3D dropped from iOS App store

☹️ I missed this one back in January, but I could sense it was coming. CambridgeSoft have dropped the iOS apps ChemDraw, Chem3D, and CDSL from the App Store. (admittedly I hadn’t heard of the last one at all). Together with this, the “Flick2Share” feature has been killed off. I never really used Flick2Share but it seems that PE are putting all their efforts in the sharing space into the updated ChemDraw Cloud, which I also haven’t really used yet. I hope to get around to fully evaluating ChemDraw Cloud at some point and reviewing it here.

deathofcdapps

ChemDraw, Chem3D, CDSL iOS Announcement © Cambridgesoft / Perkin-Elmer

I’m sad that the iOS apps are gone, particularly ChemDraw. I like the ability to quickly share structures to social media, particularly seeing as the desktop versions struggle to easily produce GIFs that retain resolution in web browsers, especially  on Twitter, and in 3rd Party Twitter clients,

[Update 2 March] However, if you have downloaded the apps to your iPad they will continue to function. Testing this morning on my rapidly ageing iPad3 the last-downloaded versions (ChemDraw 2.01, Chem3D 2.02) worked OK, except that on startup you may see an oblique message to the effect that “a sharing option could not be enabled”. I forgot to screenshot it but I presume this means Flick2Share.

 

So here is a summary of what still works. ChemDraw:

  1. Drawing, editing, saving, and (some) exporting of structures
  2. Save picture to Camera Roll
  3. Dropbox export (PDF, PNG, CDXML) works fine as previously
  4. Twitter export
  5. Export via email

What doesn’t work:

  1. Flick2Share

 

img_1207

Twitter sharing in ChemDraw for iPad still works

 

Chem3D was always a somewhat limited product compared to the desktop version, and never gained any additional features after my original mini review. This limitation was somewhat compensated for by virtue of being free. Importing structures could only be done through iTunes or downloaded protein structures from the PDB. Chem3d for iPad is a viewer application only. There are no molecular mechanics options available at all, and analysis options are few. But after a brief test the list of what works and what doesn’t is as follows:

  1. Viewing and importing of structures from the PDB
  2. Save picture to Camera Roll
  3. Twitter export
  4. Email export

What doesn’t work:

  1. Flick2Share
  2. Dropbox Export
Chem3D Twitter export also still works.

Chem3D Twitter export also still works.

Actually I don’t recall Dropbox export ever working for Chem3D, whereas it works fine for ChemDraw. As of this morning choosing Dropbox as the export function simply flips you out to the Dropbox app, if installed, to the default root directory listing page, and no option to name the file or specify a location. It just sits there until you go back to Chem3D. Nothing is ever written to Dropbox. Personally I have always preferred Pymol for visualising proteins for use online and in print,  so the loss of Chem3D for iPad isn’t as big of a deal for me as ChemDraw.

I was happy to pay around $10 for ChemDraw when it came out so I’m disappointed that it’s been abruptly dropped. It’s a peculiar strategy for CambridgeSoft/PE who evidently see ChemDraw Cloud as the future, particularly as everyone else in the app space seems to be trying to drive people away from web services and onto apps. Witness the endless pop-ups in Safari on every other web page imploring you to download and view their content in their app. An annoying UI “feature” that I earnestly implore Apple to kill ASAP.

When these apps originally appeared I saw them as principally teaching tools, given the reduced set of features and lower price point. With tablets becoming common in schools I saw possibilities for teachers and students flicking structures back and forth in pop quizzes  etc. A few people have contacted me wondering about this too, but I have absolutely no idea of what the uptake of this was in schools. Obviously PE has that information and made a business decision to drop it. I’m not yet convinced that ChemDraw Cloud is going to fit that school usage demographic either. In it’s current form its seems placed more towards the higher, content creation end of the user spectrum.

Posted in Chem, ChemDraw, Chem_Comp, iPad, tablet, Twitter | Tagged , , , , , , , | Leave a comment

ChemDraw 16.0.1, a maintenance release

chemdrawchain

Cambridgesoft/PerkinElmer announced a ChemDraw maintenance release of ChemDraw and ChemOffice 16.0.1. Apparently designed principally to address usability on the Mac platform.

ChemDraw 16.0.1 Announcement © Cambridgesoft / Perkin-Elmer

ChemDraw 16.0.1 Announcement © Cambridgesoft / Perkin-Elmer

Posted in Chem, ChemDraw, mac | Tagged , , | Leave a comment

ChemDraw 16, a second look: Running under MacOS Sierra

[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:

It works!

It works!

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.

ChemDraw 16 under MacOS Sierra

ChemDraw 16 under MacOS Sierra

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?

Posted in Uncategorized | 2 Comments

ChemDraw 16: A first look

[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 16.0.0.82. 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.

New features of ChemDraw 16, taken from the flier.

 

ChemDraw 16 new features from official flyer

ChemDraw 16 new features from official flyer

 

Versioning and Autosave.

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.

 

browse versions interface in MacOS

*This is not Chemdraw, just a PNG file in Preview

 

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.

High resolution monitor support.

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.

Some fun stuff.

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

The dreaded blue-bounded box. Your ChemDraw figure is no longer editable.

The dreaded blue-bounded box. Your ChemDraw figure is no longer editable.

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.

Round trip editing with Word 2011

Round trip editing with Word 2011

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:

Round trip editing with Powerpoint 2011

Round trip editing with Powerpoint 2011

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.

The Main ChemDraw 15 Toolbars.

The Main ChemDraw 15 Toolbars.

The Main ChemDraw 16 Toolbars.

The Main ChemDraw 16 Toolbars. Links to ChemDraw Cloud and Scifinder are circled.

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.

Posted in Chem, ChemDraw, mac, Twitter, Uncategorized | 3 Comments

BBOCS is dead, Long Live QACS? A Brisbane #ozchem conference gets borged

A couple of weeks ago I learned that the Brisbane Biological and Organic Chemistry Symposium (BBOCS) is being discontinued.

qacsannouncement

First flyer for Inaugural QACS Conference: Source: Queensland RACI Branch Newsletter

In it’s place in 2016 there will be held the inaugural Qld Annual Chemistry Symposium (QACS). This symposium will be substantially expanded from previous years and will include Inorganic, Polymer, Analytical and Environmental chemistry sessions running concurrently. Previously these other subdisciplines have had their own one-day symposia in late November/early December.

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.

BBOCS Plenary Lecturer Gender ratio 2001-2014

BBOCS Plenary Lecturer Gender ratio 2001-2014

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.

Posted in Chem, conferences | Tagged , , | Leave a comment