Home Improvements: New Features in the 2013 CSD System

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Written by

Pete Wood

Posted on

November 14, 2012

After the recent blog post on the testing of the CSD System software, I thought I’d fill you in on some more details of the exciting new features that are going to be available in this year’s release of the CSDS. The period building up to a CSDS release is always a great opportunity to review the various enhancements that have been requested by users and prioritise a selection to be included in the annual update. We can also assess whether any other software developments or research going on in the building can be harnessed to provide new functionality for the users with a bit of work.

This year, mostly in response to user feedback, the major CSDS improvements that we’ve made are in the Mercury visualiser, the Solid Form module and IsoStar (our CSD knowledge base of intermolecular interactions). The Mercury visualiser in particular has been completely over-hauled with a lot of work done on the visualisation code to improve the resolution, add anti-aliasing, improve depth-cueing, speed up rendering and provide a quicker refresh rate for large structures. As soon as you open up your new version of Mercury you should see the difference – every molecule now looks like it’s been lovingly rendered by your favourite computer animation film studio (albeit without the fur and toothy grin)!

 The same image exported at the same size directly from Mercury using last year’s release (left) and this year’s release (right) highlighting the huge improvement in visualisation performance (CSD refcode VAYXOI)
On top of the improvements made to the visualiser, we have also made a number of enhancements to our image output options. Users will now be able to generate images direct from Mercury with transparent backgrounds in PNG and TIFF format. Better control is now available for output resolution and we have provided consistent scaling of labels, lines and other objects in the view upon image resizing. A number of fixes and improvements have been made to the POV-Ray image output such as better handling of transparent objects (such as least squares planes, BFDH morphology and symmetry elements), correct handling of label positions and ability to cope with gradient backgrounds. Finally, for those of you often making molecule images for publication, we have also included an option to manually re-position each and every label (including distance and cell axis labels) so you can put them exactly where you want (or where the journal editor tells you).
Labelled image of a hydrogen-bonded dimer in CSD refcode SALOXM output directly from Mercury using the new options to manually place each individual atom and measurement label


Within the Solid Form module we have made some significant upgrades to the Hydrogen-Bond Propensity tool, which make it easier to use. In particular we have added the ability to draw a target compound to analyse (rather than having to supply a model file). Most of the steps involved in the propensity calculations have been sped up, so the whole process is now a lot faster and easier to use from start to finish. Also in the Solid Form module, we have now added the ability to calculate and output the transformation matrix relating to any and all packing similarity analyses.
Last, but not least, we have extended the coverage and data available in IsoStar. There are now eight new heterocyclic central groups added to the intermolecular interaction knowledge base including tetrazolate, imidazoline and squarate.  We have also now increased the maximum number of hits included in scatterplots so that the software can cope with up to 10,000 contact atoms rather than a maximum of 5,000 atoms, which will improve the plots and contour maps for common interactions.
Hopefully this has suitably whet your appetite for this year’s CSD System release and, if so, you should not have long to wait before receiving it. We are now packaging up the discs and are on track to start shipping out the software in the week beginning the 19th of November.​


CSD System (45)