CDS email message - CDS/03/12/13/

Sent 03 Dec 2013

Further improvements to CrystalWorks


Please give feedback on recent modifications to the interface

We have been working on tidying aspects of the CrystalWorks interface.
The idea has been to make it less complicated and eliminate some of
the formatting problems reported for a number of browsers as operating
systems. The aim has been to improve the display on Linux, Android and
iPad platforms. We encourage users to give feedback on their favoured
systems. In particular we would like to eliminate any annoying scroll
bars and other artefacts which have tended to crop up in the past. 


The procedure to generate 2-D diagrams has been improved

There are now some differences in the way that 2-D diagrams are
generated. We access the National Institutes of Health site in the USA
to generate the 2-D diagrams from InChI codes. These codes are
generated from component molecules with in the 3-D structures. For
standard InChIs there is a "normalisation" stage in the generation.
The idea is to convert to a "standard" tautomer. The choice of
tautomer may seem quite arbitrary. We now switch off normalisation for
the 2-D diagram stage. It is, however, retained when searching over
Data Aggregators.


The JAVA option has been removed for structure display

Traditionally CrystalWorks has used JMol for structure display. JMol
uses JAVA. More recently JSmol has become available. This uses HTML5
and works well on all modern web browsers.

At the same time the original JMol is becoming an increasing problem
to may users because of the increasing numbers of security alarm
appearing for JAVA. This situation is not likely to improve. For this
reason we have decided to drop the JMol/JAVA option. 


See link to related newsfiles and broadcast messages:

http://cds.dl.ac.uk/cgi-bin/news/dispm?2013-10-30-b_all_users

http://cds.dl.ac.uk/cgi-bin/news/disp?icsd

http://cds.dl.ac.uk/cgi-bin/news/disp?crystmet


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