CDS News - CrystalWorks   [updated 05 Dec 2014]

CrystalWorks improves and extends the capabilities of CrystalWeb.
CrystalWeb has now been withdrawn whilst CrystalWorks continues to be actively developed.

Please provide us with reports about any errors and problems.
All comments, suggestions and general feedback are most welcome (cdsbb@stfc.ac.uk)

The total number of entries from all databases is now 1,123,985
EMBL-EBI UniChem has been added as a new Data Aggregator

See details below:

Item added 05/12/14

Links to EMBL-EBI UniChem are now provided

CrystalWorks (and prior to that CrystalWeb) already includes links to various data aggregator sites (see Items added 11/12/12 & 05/09/10).

We are pleased to announce the addition of the EMBL-EBI Unichem as a new aggregator site linked to CrystalWorks.

Unichem makes links based on chemical structure to a wide range of information sources. These include ChEMBL, ChEBI, PDBe (Protein Databank in Europe) and PubChem. It has many useful features including cross references to related structures which have modified stereochemistry, isotopic substitution or differing protonation.

This has allowed us to simplify the "Choose a site to search" section within the "Literature links & Data aggregators" sub-menu. It now includes only "NIST WebBook" and "ChemSpider" together with UniChem.

UniChem is undepinned by a large-scale non-redundant database of pointers between chemical structures and EMBL-EBI chemistry resources. In addition it provides centralised mapping for external resources. These currently include PubChem, ZINC, SureChem, etc., and it is anticipate additional ones will be added later.

For further details including a full list of data sources Click on the "Links..." menu bar.

The UniChem links have been implemements for CrystalWorks accessed directly from the CDS/DL website. Changes will be made to the version of CrystalWorks available via the RSC portal in due course.

Item added 22/11/14

New links added to pulldown menus

Links to Crystallographic Open Database (COD) searching using CrystalWorks and the links example page (see Item added 21/10/14) have been added to the Access Data menu on the home and other CDS/DL pages.

Please note that you do not need to have a CDS/DL username to search the COD database using CrystalWorks.

Item added 24/10/14

The page about external webpages has been improved

The text has been been expanded in the webpage and further examples have been added.

We have also added more information on searching the COD database via the COD homepage and via CrystalWorks.

Item added 21/10/14

Linking external webpages to CrystalWorks - use of COD database

There is a prototype page linking structure references to CrystalWorks. This page illustrates ideas to allow links between external webpages and the CrystalWorks system resident on the CDS/DL server.

For further details Click on the "Links..." menu bar.

The aim is to help authors of external webpages who have identified a list of interesting structures from the major 'small molecule' and materials crystallographic databases.

Using a simple interface they will be able to transfer the related collection codes, together with some brief annotational details, to the CDS/DL server. CrystalWorks then provides its full structure and bibliographic display and other facilities.

In the examples shown on the page structures are taken from the Cambridge Structural Database (CSD) and the Inorganic Structural Database (ICSD). In addition there are also entries from the Crystallographic Open Database (COD).

For further details Click on the "Links..." menu bar.

Please note that the addition of data from COD is a recent development within CrystalWorks. Further developments are underway and the COD dataset is not fully up to date.

Item added 15/07/14

RSC version more closely coupled

We have made modification such that the version of CrystalWorks available through the Royal Society of Chemistry web site is the same as that available via the Daresbury site.

This means that all software and data updates will be applied simultaneously on both sites. Until now changes to the RSC version may have lagged behind those applied to the CDS/DL.

Item added 15/07/14

CrystalWorks now uses JSmol 14.2.2

JSmol has been upgraded to version 14.2.2 from 14.0.13. Please report any problems you may encounter.

Item added 14/07/14

Entries for CrystMet with no coordinates now flagged

A problem where entries for CrystMet without coordinates were not correctly flagged was inadvertently introduced in the 11/07/14 update. This has now been fixed.

Item added 11/07/14

The latest CrystMet data update 5.1.0 is available

This adds 8,194 new entries and brings the total number of entries from all databases to 1,123,985

Item added 07/07/14

Data from Cambridge May 2014 Update now available via the RSC site

Item added 06/07/14

Data from Cambridge May 2014 Update now available

This adds 23,048 entries, bringing the number of entries from the CSD to 717,903. It brings the total from all databases to 1,118,670.

Note this data update is currently only available for access through the CDS/DL website. Access to the new data via the RSC service will be implemented shortly.

Item added 05/07/14

Changes to CrystalWorks structure display

There have been a number of changes to the underlying JavaScripts which are incorporated into the CDS/DL version of CrystalWorks. In particular this now uses JSmol 14.0.13 - the previous version was 13.3.9.

Our implementation of JSmol now mades use of "anti aliasing" (dithering) as the default option. Hopefully this should remove some display artefact (e.g. "zaggies") which have been a cause of annoyance. Unfortunately this slows manipulation of structures on Tablets and so anti-aliasing on/off radio buttons have been added to the Structure display menu.

Changes have also been made to deal with the absence of mouse option for tablets. Here again there are more radio buttons. They change the way the touch (mouse down) and drag works. The options are Translate, Zoom, ZRotate & Rotate.

Note these changes are currently only available for access through the CDS/DL website. Changes to the RSC implementation will be made shortly.

Item added 09/06/14

A bug with coordination environment searching has been fixed

We have discovered that the coordinate environment search facility was broken as a result of the 05/06/14 upgrade. Searches produced spurious null Hits Lists. This problems has now been fixed.

Please repeat any searches which may have been affected by this problem. Apologies for any inconvenience.

Item added 05/06/14

A problem with element count searching has been fixed

There have been reports of problems with "element count" searches for the Cambridge Structural Database. The element count is defined as the number of different element types contained within all components of structure.

Thus the Refcode LIRBOF has the formula "1.5(C10H8N2), C7H8O2" and the element count should be 4. For a number of similar multicomponent CSD entries the element count used by CrystalWorks was calculated incorrectly. For this example the value was calculated as 5. This problem has now been fixed.

It is also worth remembering to take care when using the "Elements in formula" search field. In the example formula above a valid search would be "c10 h8 n2 c7" (the ordering is not important and you need not include all the atoms). However, searching on "C10H8N2" would fail. The search field is case insensitive but including spaces is important.

Item added 05/06/14

CDIF entries have been renumber

We have recently discovered that there were a number of duplicate collection codes for entries in the Crystal Data Identification File. This resulted in incorrect display for the affected entries. This problem has been fixed by re-assigning codes for CDIF entries to correspond to positions within the CDIF database. The new CDIF collection codes range from 1 through to 78493.

Please contact cdsbb@stfc.ac.uk if this created problems for you ar you spot any anomalies.

Item added 23/05/14

The latest update is now available via the RSC site

Item added 23/05/14

ICSD data update 2014/1 now available in CrystalWorks

This adds 2,961 entries making a total of 169,800. It brings the total number of entries for all databases to 1,093,721.

Note this data update is currently only available for access through the CDS/DL website. Access to the new data via the RSC service will be implemented shortly.

Please contact us via cdsbb@stfc.ac.uk if you encounter any problems relating to this update.

Item added 23/03/14

Problems with 2-D structure display have been fixed

CrystalWorks generates 2-D structure diagrams (see Item added 20/09/13). Improvements were made (see Item Added 02/12/13). Unfortunately these improvements were dropped recently for a number of entries.

This problems has now been corrected. However, please contact us on cdsbb@stfc.ac.uk if you detect any 2-D structures which look incorrect as compared to the 3-D display.

Item added 19/03/14

The latest update is now available via the RSC site

Item added 18/03/14

Data from Cambridge February 2014 Update now available

This adds 19,566 entries, bringing the number of entries from the CSD to 694,855. It brings the total from all databases to 1,089,790.

We have received report of issues with Cambridge "no coordinates" entries. In some cases these were not flagged correctly as such for Hits Lists in the Top Level menu. Also the system would occasionally hang when attempting to access the lower level menus.

We believe this has now been succesfully corrected with this latest update. However, please contact on cdsbb@stfc.ac.uk if you suspect any continuing problems.

Note this data update is currently only available for access through the CDS/DL website. Access to the new data via the RSC service will be implemented shortly.

Item added 23/02/14

Southampton Archive now included in the CSD

Publically available structures within the the Southampton eCrystals Repository are now being abstracted by Cambridge Crystallographic Data Centre, and have appeared in the latest CSD update.

We believe there is no need for duplication of such entries and no longer include Southampton entries separately within CrystalWorks. The "Load Soton Repos." button has now been removed from the CrystalWorks Top Level menu. To check on the current public Southampton Archive within CrystalWorks use the standard Bibliographic Menu search. For instance type "southam" into the Journal field.

Item added 23/02/14

ASAP articles now included in the CSD

ASAP (As Soon As Publishable) articles are now appearing in Cambridge Structural Database releases. This means that for structures published in a number of major journals there is no need to delay until an article appears in print form. The drawback is that year, volume and page information is not immediately available.

At present you can search for ASAP articles within Crystalworks by searching with the publication year set to 0 (this may change in the future). There are currently 1103 ASAP in the CSD. You can, of course, also refine your search with a specific journal name.

Year/volume/page information will be added to the CSD for the ASAP article as it becomes available. At present it not clear on what time scale this will happen, but you can, of course, check the article DOI for updates to its year/volume/page assignment.

Item added 19/02/14

The latest update is now available via the RSC site

Item added 14/02/14

Data from the Cambridge 2014 Full release is now available

This adds 17,294 entries making the total from the CSD 675,301. It brings the total number of entries for all databases to 1,070,532.

Note this data update is currently only available for access through the CDS/DL website. Access to the new data via the RSC service will be implemented shortly.

Item added 24/12/13

Some author fields reformatted in ICSD

The latest ICSD update included certain entries with full author forename information rather than simply initials. This created problems for our data uploading procedure. For instance a number of author fields were no longer searchable and some author display fields where corrupted.

For data consistency full forename have now been converted to initials, and all author fields should now be fully searchable.

Please repeat any searches where you suspect there may have been problems. Report any continuing problems to cdsbb@stfc.ac.uk.

Item added 16/12/13

Coordinate searching now available for all entries

There have been reports of problems with coordinate environment searching following the recent data update. Searches failed to find certain entries within the ICSD and CrystMet databases.

We have reprocessed the coordinate search files and the problems now seem to have been fixed.

Please repeat recent searches and report any suspected continuing problems to cdsbb@stfc.ac.uk.

Item added 14/12/13

ICSD data update 2013/2 now available in CrystalWorks

This adds 5,815 entries making a total of 166,842. It brings the total number of entries for all databases to 1,052,283.

Item added 03/12/13

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 many users because of the increasing numbers of security alarm appearing for JAVA. This situation is not likely to improve. It is for this reason we have decided to drop the JMol/JAVA option.

Item added 02/12/13

The procedure to generate 2-D diagrams has been improved

There are now some differences in the way that we generate 2-D diagrams (see Item added 20/09/13). 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 within 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 (see Items added 20/09/13 & 02/04/13).

Item added 01/12/13

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 and operating systems. A primary 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.

Item added 19/10/13

CrystMet 4.8.0 is now available again via the CrystalWorks

This bring the total number of searchable entries available to CrystalWorks back to over the one millions mark.

Item added 08/10/13

The National Institutes of Health server now back

The National Institutes of Health server is operating correctly again. The 2-D display facility in the CrystalWorks is now working properly.

Item added 05/10/13

Problems with the National Institutes of Health server have returned

Problems with 2-D structure diagram display have returned (see Item added 2/10/13). Hopefully full functionality will return shortly. We will post any further information as it becomes available.

Item added 04/10/13

Full search functionality has been restored for current CDS/DL users

We are pleased to announce (see Item added 3/10/13) that plans are now in place for the Royal Society of Chemistry to make CrystalWorks available via the RSC/NCDS Portal at some point soon.

In the meantime full CrystalWorks search functionality has been restored for established CDS/DL users who have retained their registration. Fuller integration within the RSC/NCDS system will follow at a later stage.

How to logon to CrystalWorks

Users within the STFC network domain (those on site at Daresbury, Rutherford or the Diamond Light Source) can still login using the form on the CDS/DL homepage. This option remains unavailable outside the domain. However, wider access to CrystalWorks is available again from most CDS webpages (including this one).

Select a CrystalWorks option via the Access Data link. When the Top Level Menu appears you can click the "Username logon" button and enter your CDS ID and password.

Database components available

At present CrystalWorks provides full search capabilities covering


With the current arrangements the RSC holds the national UK academic network licences for CSD & ICSD.

CrystMet from Toth Information System was temporarily withdrawn (see Item added 18/04/13) from CrystalWorks. The RSC expects to have a new network licence in place shortly, and CrystMet will be restored as a searchable component.

Password changes and new registrations

If you have forgotten your CDS/DL password you can get a new one. Simply click on the "Forgot Password?" link present on the CDS homepage.

To change your password to one of your own choosing or update your registration details you need to be within the STFTC network domain. Likewise you need to be with the STFC domain to register as a new CDS/DL user.

However, we hope to be able to restore these options shortly.

Item added 03/10/13

There are plans to make CrystalWorks via the CDS/RSC Portal

It is hoped that arrangements can be made to provide CrystalWorks access via the Royal Society of Chemistry National Chemical Database Service (NCDS). This will mean that full search functionality will become available to all eligible UK academic users. This will including those outsite the STFC network domain.

Further information will be made available as it becomes available.

Item added 02/10/13

Problems relating to the lapse in US government funding

Problems relating to the lapse in US government funding have affected various web sites in the United States.

There have been recent problems with our 2-D structure diagram procedure (see Item added 20/09/13). This was related to problems with the operation of the National Institutes of Health cactus.nci.nih.gov site. This seems to have been resolved at present.

Please note that the NIST WebBook is currently not in operation. All links to that site now fail.

We will add further items if we receive further information on the US funding situation.

Item added 20/09/13

Changes to various CrystalWorks pages

Changes have been made to various pages within Crystalworks. In particular there are now improvements to the initial main menu start up procedure and to the "Links & Data aggregators" sub-menu. This sub-menu now includes 2-D chemical diagrams. We have also tidied the section which links to the aggregators sites. Two new links have been added.

Links to the RCSB Protein Data Bank

There are two new links to the RCSB Protein Data Bank site. They point to information on "small molecules/ligands" which are present in refined protein structure. The first link points to relevant protein structures. The second gives chemical details of the ligands provided by the RCSB/PDB site.

2-D structure display has been added

As mentioned above we have added a 2-D display facility in the "Links & Data aggregators" sub-menu. This is currently makes use of a web service provided by the National Institutes of Health cactus.nci.nih.gov site, and the diagrams are generated "on the fly".

The 2-D structures are generated from IUPAC International Chemical Identifiers (InChIs) derived from the 3-D structure information available for each database entry. A separate InChI (and 2-D diagram) is generated for each chemically unique entity within the crystal structure.

At present the procedure seems to work well for most organic structure, but is less satisfactory for organo-metallic, inorganic and metallic systems.

Item added 29/07/13

CRAD & Powder Pattern Generator problems fixed

There have been recent problems switching to CRAD and Powder Pattern Generator mode in the "Coordinates and Generators" sub-menu (see Items added 22/04/13 & 17/04/13).

These have now been fixed. Apologies for any inconvenience.

Item added 03/07/13

Problem with changed atomic radii fixed

The "Change atomic radii" in the "Structure display" sub-menu allows you to edit molecular connectivity by modifying atomic radii away from their default values.

In most circumstance only one atom type needs to be changed. We have discovered a bug which could sometimes create problems when the radii of multiple atoms types were changed at the same time. This has now been fixed.

Item added 02/07/13

Problem with filtering Hits Lists fixed

Apologies for recent problems with the "Filter Hits List" page - the entry selection option has not been working for the last several days. This error has now been fixed.

Item added 30/05/13

The May13 CSD data update added

This adds 13,610 new entries. It brings the total number of entries for all databases to 897,327.

Item added 17/05/13

General national login access to CrystalWorks has now been withdrawn. However, access via the 'Login first..' form on the CDS homepage remains available to those within the STFC domain.

We will broadcast information on future CrystalWorks availability if and when circumstances change.

Item added 16/05/13

Reminder - General CrystalWork login access will cease tomorrow.

General national login access to Crystalworks will be withdrawn on the 17 May. This is scheduled to happen around noon time. See Item added 07/05/13 for further details.

Item added 15/05/13

Non-coordinate ICSD renumber

We retain a collection of older ICSD entries which do not include coordinate data for use within CrystalWorks. These entries have been removed from the more recent ICSD updates of ICSD-WWW and the FIZ Karlruhe internet version made available via the RSC portal. All entries in question contain cell dimension data and are fully searchable They include a range of novel phases which may not be available elsewhere.

We have noticed some duplicate numbering for this ICSD collection, which results in display problems for multiple hits. All these entries have been renumbered. They now cover the range nc1-nc2331, and we believe that this has resolved the display problems.

Item added 07/05/13

General CrystalWork login access will be withdrawn from 17th May

General national login access to Crystalworks will be withdrawn from the 17 May. Apologies for problems this will create.

This is required so we can comply with the conditions of our current database licences. Hopefully arrangements can be made to restore full access at some point in the future. We will post further information as it becomes available.

Please note that the "Login first" form on the CDS Homepage will remain available to registered CDS users if they are in a position to access the service from within the STFC network domain (Daresbury, Rutherford and the Diamond Light Source). The "Login first" form will continue to provide a method of logging in to CrystalWorks. This covers both local STFC and DLS staff as well as visitors to the sites.

CrystalWorks searching is available only to logged on users. CrystalWorks will, however, remain available in "demonstration" mode. This means you can still view the two sets of representative structure entries which we will continue to provide on the CrystalWorks Top Level Menu. Full CrystalWorks functionality is then available for all of these sample entries.

Item added 04/05/13

The ICSD data update 2013/1 added

This adds 6,637 new entries. It brings the total number of entries for all databases to 884,501.

Item added 03/05/13

The Feb13 CSD data update added

This adds 13,610 new entries. It brings the total number of entries for all databases back to 880,151. This follows the recent loss of 150,125 entries following the (hopefully temporary) withdrawal of CrystMet.

Item added 22/04/13

CRAD: Crystal RADial distribution calculation

A CRAD generator is now in place. It is also available via the "Coordinates and Generators" sub-menu.

This is an interactive option which reads crystal data. The crystal asymmetric unit is expanded by applying space group symmetry and lattice translations. Distances involving a selected central atom are calculated and sorted for display.

At present it gives very similar output to that produced by the old command line CRAD program which ran on the CDS server for logged on users over any years.

Changing the output options would be relatively easy to meet the current needs of EXAFS and other users. We welcome any feedback on changing and improving the output format.

Item added 18/04/13

The CrystMet database system has been removed

The CrystMet database has been removed from CrystalWorks. This is because our previous licence covering networked provision has expired, and new arrangements are not as yet in place.

It is hoped that suitable arrangements can be made to restore this useful facility as soon as possible.

Item added 17/04/13

Powder diffraction generator now available

A powder diffraction generator is now available within CrystalWorks. This facility is provided via a link to the ICSD-WWW software. It uses the code developed by P. Hewat and A.W. Hewat which makes use of the Lazy Pulverix (Benjamin Nunes) program.

You can access this generator from what was the "Coordinates download" sub-menu. This sub-menu has now been renamed "Coordinates and Generators" to reflect this upgrade.

Also note that "DISTXR" output is now the first in the list of format outputs. There have also been changes. The crystal space group symbol (Hermann-Mauguin) and number are now given. The point group (Schoenflies) is given for each unique atom position.

We also expect to have a Crystal Radial Distribution Calculator added to CrystalWorks quite soon. This will be based on the CRAD program which was made available as command line program on the old CDS system. CRAD was of particular value to the EXAFS and other communities.

Item added 02/04/13

Linking to data aggregators has been improved

CrystalWeb already includes links to various data aggregator sites (see Item add 11/12/12). Problems have been experiences with a number of entries on the EMBL-EBI site. This affected compunds which used to be in both the ChEMBL and CheEBI databases. Where entries (e.g. Octsulfur, S8) had been removed from the ChEMBL database they continued to give spurious hits, but with no link to the CheEBI.

This problem has now been fixed.

Item added 09/03/13

CrystalWorks logins have been reinstated for CDS/Daresbury users

We have reinstated login access for CrystalWorks for those who have retained a valid username for the original National Chemical Database Service at Daresbury.

Please note that this facility is currently not available, by default, to anyone who has only used the more recent CDS/RSC system. Also this Crystalworks service is made available on a temporary basis only and may well have to be withdrawn after the 31st of this month.

Logged on users have access to the full CrystalWorks search facilities - you are not restricted to the sets of demonstrations Hits Lists available prior to login.

How to login to CrystalWorks

Login access to CrystalWorks is available on most CDS webpages. Select a CrystalWorks option via the Access Data link. When the Top Level Menu appears you can click the "Username logon" button and enter your CDS ID and password.

Please note that access to other database systems at Daresbury (via use of the CDS homepage login form) continues to be restricted to users within the STFC domain.

Item added 24/02/13

Article titles are now included

Article titles are are now given on the Links & Data aggegators page where they are available. This information is extracted via CrossRef.

Item added 05/02/13

JSmol is now available for structure display

The Jmol structure display system is now available via the new "JSmol" system. JSmol provides an alternative to the Jmol applet within CrystalWorks.

This means that Jmol functionality is now available on system which do not support Java. In particular this includes tablets and phone (iOS, Android) as well as workstations where Java may not have been installed because of security concerns.

JSmol can provide most of the graphic functionality of Jmol using JavaScript. It, however, requires the graphics capabilities provided by HTML5. Most modern browsers will provide these feature, but you may encounter problems with earlier versions of Internet Explorer.

Both the JAVA and HTML5 version are now available by clicking on Access Data at the left of the top pulldown menu on all CDS webpages.

Please report any problems you may encounter to cdsbb@stfc.ac.uk

Item added 02/01/13

Access to the demo version of CrystalWorks continues

Access to the demo version of CrystalWorks continues. However, to login and use its full search capabilities you need need to be accessing the system from either the Daresbury or Rutherford site (including the Diamond Light Source).

Item added 11/12/12

Linking to data aggregators has been improved

CrystalWeb already includes links to various data aggregatore sites (see Item add 05/09/10). We have removed the link to the Chemical Structure Lookup Service (CSLS) and added a link to the PubChem site instead.

We have also added a combined link to the database on the EMBL-EBI site (ChEMBL and ChEBI). This will follow a link to the ChEMBL database where such a link exist. If there is no such link the EBI database will also be searched.

In most cases we recommend that you select PubChem or the EMBL-EBI site first before trying ChemSpider.

Item added 10/12/12

CrystalWorks can now be used on browsers without Java

The Jmol molecule display component embedded within CrystalWorks requires Java to be enabled on your browser. Certain systems (e.g. tablets such as the IPad) do not support Java. It is also possible that your browser will disable Java because of security concerns if you have not installed the most recent Java update.

Previously Java had to be installed even for non-graphics features of CrystalWorks to work properly. We have made modifications such that searching and bibliographic display of Hits sets can now function correctly without Java.

We are investigating non-Java based graphic options (e.g. JsMol) in cases where the use of Java is impossible.

Item added 05/11/12

The ICSD 2012/2 data update has been added

This data is also available for users of CrystalWeb

Item added 27/09/12

Racemic pairs are correctly handle for data aggegator site searching

CrystalWorks now uses both components of any racemic pair when generating links to data aggregator sites (currently ChemSpider, ChEBI, NIST and CSLS are available). This affects chiral molecules included in crystal structures refined with non-chiral space groups. Previously only one component of any racemic pair would have been given for such structures.

We have added some extra entries to the end of the collection of Example Hits available from the Top Level Menu of CrystalWorks.

The new example entries include a racemic crystal structure of Thalidomide (csd thalid10). This entry now has links for both the D-Thalidomide and L-Thalidomide molecules (previous only a link for D-Thalidomide was provided). The other 4 examples are for tartaric acid. There are two chiral structures (tartal and tartac). The two non-chiral structures are racemic (zzdui01) and the internally compensated stereoisomer (tartam).

Please note that both components of any racemic pair are not as yet shown for the "Unique Molecule Set" option within the Structure Display menu for CrystalWorks.

Item added 07/09/12

The Aug12 CSD data update has been added

This smashes the One Million Entry milestone in CrystalWeb and CrystalWorks

Item added 04/09/12

Format improvements for various browser

There have been a number of modifications in the way that formatting is handled (changes to CSS style sheets). These changes are primarily intended to improve formatting for the various versions of Internet Explorer, but may affect othe browsers.

To ensure that you are using the latest versions of the CSS style sheets we recommend that you use your Refresh button for the Top Level Menu of CrystalWorks.

Item added 03/09/12

Changes to Top Level Menu and Filter options

There have been changes to the Top Level Menu when you first enter the CrystalWorks package. These provide some additional explanatory details about loading sample Hits Lists.

There have also been improvements in the edit facilities available for your selected Hist List. To access these facilities click the "Filterer Hits List" button. The new edit facilities should be self explanatory, but contact us via cdsbb@stfc.ac.uk if you have any queries/comments.

Item added 26/08/12

Entries for CrystMet with no coordinates now flagged

A problem where entries for CrystMet without coordinates were not correctly flagged has now been fixed in CrystalWorks - the problem remains for CrystalWeb.

Entries without entries no longer display the "Coordinate download", "Structure display", and "Output CIF format via Socket" links.

Item added 06/08/12

Backend server problems fixed

A disk on the server providing searching facilities for CrystalWorks and CrystalWeb failed. The system was transferred to a new server and was fully functional again at 9.30am 6th August.

During the downtime CrystalWorks may have given spurious empty hits lists for searches (CrystalWeb correctly generates an error message under these circumstances). If you suspect problems rerun your searches.

Apologies for any inconvenience.

Item added 27/06/12

The latest CrystMet data update 4.8.0 has been added

This brings the total number of entries from all databases to 993,552

Item added 06/06/12

The May12 CSD data update added

This brings the total number of entries from all databases to 985,452

Item added 11/05/12

Changes to text searches

There have been some slight modifications to the way text searches are handled. Multiple blanks are now converted to single blanks and leading and trailing blanks are removed prior to any searching. Before this change was made text fields with any trailing blanks accidentally included yielded zero hits.

Please report any suspected problems which my have arisen as a result of this change. Note that this modification has not as yet been implemented for CrystalWeb.

Item added 03/05/12

The 2012/1 ICSD data update has been added

This brings the total number of entries from all databases to 970,480

Item added 05/03/12

The Feb12 CSD data update has been added

This brings the total number of entries from all databases to 962,617

Item added 24/02/12

We remind users that "reduced" cell searching is possible covering all the component databases (currently 946,375 entries).

In CrystalWorks this can be combined with additional contraints such as elemental composition.

Item added 20/02/12

CrystalWeb and CrystalWorks now restored

A replacement disk has been installed and the CrystalWeb server database rebuilt from scratch. Please report any unexpected behaviour.

Sorry for all the inconvenience

Item added 13/02/12

CrystalWorks search broken because of Oracle server problems

CrystalWorks searching currently gives spurious zero Hits Lists. This is unlikely to be fixed before the weekend of the 18th February.

Please follow the latest news on the CDS homepage and on Twitter.

Item added 10/01/12

There has been some reformatting

There has been some reformatting of the Top Level menu and Filter Hits List page. Hopefully these changes are self explanatory.

Please contact cdsbb@stfc.ac.uk if you encounter problems or have any suggestions/comments.

Item added 01/01/12

A filter facility for Hits Lists has been added

A new filter/edit facility has been added. This allows you to retain a sub-set of your current Hits List.

To use the facility click the new "Filter the current Hits" button on the Top Level Menu page. This take you to a new page. You can scroll through the full details for each entry and flag any relevant ones. You have the choice of either deleting or retaining your flagged entries. The process of removing unwanted entries can be performed in stages.

When the filtering process is complete you can then return to the Top Level with your filtered Hits Set. The ordering of the entries is the same as for the Hits List display at the Top Level. If you wish to change the sort criterion for the entries you need to do that at the Top Level.

This facility is only available for logged on users.

Item added 12/12/11

The number of entries in the Hits List is now flagged

There has been further reformattting and more popup warnings have been replaced by less intrusive alternative means.

A running total of the number of entries in the current Hits List is displayed. This is updated as any new entries are added or removed.

Item added 08/12/11

Improved version of CrystalWorks is now the default

A new version of CrystalWorks is stable (see Item added 23/11/11) and is now the default.

The new version has many improved features

There are major changes to the Top Level and some of the lower menus:

* A number of popup messages have been removed and you should see fewer scroll bars in the display menus.

* There are differing menu options depending on whether you are already logged in with a CDS username or not - for instance you only get the search option if you are a logged in user.

* If you are not logged on there are details of how to register as a CDS username and links to full details of the Service.

* There is now a logon and also a logout option.

* You are not presented with a sample Hits List when you enter CrystalWorks.

* There are new buttons to up load the Selected Example Entries or all entries in the Southampton Repository to the Hits List window - these option are available for both registered and non-registered users.

* There is a totally new facility which lets you control the ordering criterion and display field options for the Hit List window.

Please contact us via cdsbb@stfc.ac.uk if you come across any problems with the new version. As always suggestions for improvements and new facilities are welcome.

Item added 25/11/11

The ICSD 2011-2 data update has been added

This brings the total number of entries from all databases to 946,375

Item added 23/11/11

Default version of CrystalWorks is restored

The older version of CrystalWorks has now been restore. Apologies for any inconvenience caused.

Please note that the development version will remain available (see Item dated 22/11/11). This new version will become the default when a number of minor display problems have been ironed out.

In the interim you are encouraged to test the new system, report any problems, and make comments and suggestions.

Item added 08/11/11

System freeze for Southampton Respository entries

There has been a recent problem when attempting to retrieve full structural details for entries within the Southampton Repository.

This affected the "Jmol structure display", "Links & data aggregators" and "Coordinates format download" menus. In certain cases the CrystalWorks system would freeze completely.

This was related to a system misconfiguration at our end when attempting to access the Southampton server. This problem should now be fixed, but please contact us if you continue to encounter any difficulties.

Item added 20/10/11

The November CSD data update has been added

This brings the total number of entries from all databases to 944,312

Item added 22/08/2011

The CSD Aug11 data update has been added

The total number of entries from all databases is now 935,223

Item added 20/08/11

Further display problems have been fixed

Further problems with structure display have been fixed. The problems appeared to have affected a limited range of structures. Any example was Kaolinite using the non-standard C1 setting for space group #1.

If you suspect other problems structures please do report them.

Item added 09/08/11

Problems with structure display has been fixed

We have been informed of problems with the Jmol structure display. In some cases an incomplete of set of molecules was produced for the initial single cell display option. Using the multiple cell option corrected this problem.

It is believed that the error was introduced around 03/08/11. It was corrected 07/08/11. If you suspect that you have encountered this problem we recommend that you repeat your query searching.

If you encounter any clearly incorrect or unusual features within the CrystalWorks Jmol display, please report these back to us.

Apologies for any inconvenience caused.

Item added 07/08/11

Greek letter and subscript/superscript display

There have been some further improvements to the display of Greek character and subscripts and superscripts within compound names and formulae. These applies mainly to entries from the Cambridge Structural Database. For instance atom positions labelled by a mixture of roman and greek characters to handled more reliably. Charge labels within formulae are also handled better.

It likely that some problems remain. Please report any suspicious entries to cdsbb@stfc.ac.uk

Item added 28/06/11

There is an ICSD data update

This brings the total number of entries from all databases to 919,389

Item added 01/06/11

Improved query modification is now available

It is now possible to view your retrieved hits at the top level and then modify your search criterion. Previously you could only check on the number of hits before opting to modify a query (see Item added 13/04/11).

Please test this facility and inform us of any problems you may encounter and send suggestions for future modification.

Item added 24/05/11

There is a Cambridge data update

This brings the total number of entries from all databases to 914,741

Item added 13/04/11

Modification of searches is now possible

You can now perform a database search and modify your your search in the light of the number of (or absence) of hits you retrieve. You do do not need to re-enter the entire search from scratch.

Item added 14/03/11

There is a Cambridge data update

This brings the total number of entries from all databases to 899,947

Please inform us of any problems you may encounter

Item added 27/01/11

There is a Cambridge update

The new Cambridge Release is now available within CrystalWeb. This brings the total number of entries from all databases to 884,489.

Item added 08/01/11

CrystalWorks now allows the reduced cell search option

The Reduced Cell option has now been added to the system. The "Direct cell" menu has been replace by the "Cell and crystallography" menu. This incorporates both the direct and reduced cell options as well as space group, Bravais lattice, R-factor,and Z number searching.

Item added 05/01/11

CrystalWorks now incorporates database searching

Searching is now fully integrated within CrystalWeb. You do not need to run a CrystalWeb search session within your session and then access the corresponding Hits List as a totally separate operation.

Simply click the "CrystalWeb Search" button. When you have completed your search the hits will be transferred automatically when you return to the Top Level Display menu.

The search options correspond roughly to what you get with the CrystalWeb "Comprehensive" search form. It takes you through the following menus sequentially:

* Top Level and database selection
* Bibliographic
* Journal title
* Formula & compound name
* Coordination
* Direct cell

You can mix and match, filling in details to any or all of these as you go through. Note that the Coordination search was not included within the CrystalWeb Comprehensive menu (there is a separate "Formula and Coordination Search" form). We hope to add the "Reduced" cell option as soon as possible.

If you wish to search for a journal (or group of journals - probably useful for e.g. ChemComm and JCS Dalton) add a journal title substring in the Bibliographicic menu. The journal title menu now allows you multiple choices. This is a change from what was available using the old CrystalWeb system.

Item added 15/12/10

The CrystalWorks webpage is available

A draft version of the CrystalWorks webpage is now available. This webpage will be updated and refined. Go to this page to view screenshots of the current CrystalWorks system. Click the Links banner to access the webpage and other related pages and News Items.

Item added

Item added 11/12/10

CrystalWorks is available for public use

CrystalWorks is now available as a beta release for wider evaluation. To use the system click on Access Data at the left of the top pulldown menu on all CDS webpages.

Please inform us of any problems you may encounter.

Item added 30/11/10

Litref Hits sets can now be accessed

The literature links (Litref option) as output using the CDS implementation of the Cambridge ConQuest system can now be accessed by CrystalWorks.

Item added 23/11/10

Viewing CrystalWeb hits is now possible

It is now possible to view the Hits list from a prior CrystalWeb search session. To get this functionality you will, of course, need a CDS username.

There is also an option to call up an embedded CrystalWeb search session within CrystalWorks. This is a provisional arrangement. Proper integration of CrystalWeb database searching will be added in due course.

Hits are sorted by date and journal. Further sort option are planned as future developments.

Item added 22/10/10

Formatting changes made

There have been further changes to page layout. Display of Greek character and subscripts and superscripts within compound names has been improved.

Item added 03/10/10

Jmol upgraded to 12.0.15

Jmol has been upgraded to Version 12.0.15. This will make it slow to load on the first access to CrystalWeb. Please allow the Java Applet time to download and the glucose molecule to appear before clicking the "OK" button.

Item added 27/09/10

Performance and reliability has been improved

There have been a number of developments with CrystalWork. The main one is that the start up time should now be much faster. This has had one or two knock on effects, and Jmol problems with the with the Opera browser are being investigated. Other browser seem to be fine, but feedback is requested on the behaviour when testing with platforms other than Windows XP.

Item added 05/09/10

Linking to data aggregators has been improved

Test links to the ChEBI site and NIST Chemistry WebBook have been added in addition to ChemSpider. I It was initially thought that ChemSpider would be sufficient since it gives links to the other two. This is probably the case for the NIST site. However, problem ChEBI entries have been spotted some which do not have links from ChemSpider. These include P4 (icsd 406793) and S8 (icsd 66517). There may be good reasons here. Does anyone have information on this apparent problem?

In addition entries without coordinate data are now handled in a better way. See for instance: csd acrin03.

Problems with the tidy up procedure for space group symbols have now been corrected. Symbols should now be consistent other the various database. Also the were problems for P1 and P-1 (they showed as P and P-). However, please report any odd symbols you may encounter.

Item added 22/08/10

CrystalWorks released for initial testing

CrystalWorks is available for testing by a limited number of users.

Most CDS users are familiar with CrystalWeb, ICSD-WWW, ConQuest and related crystallographic database systems.

We are currently working on CrystalWorks, which will enhance and at some point totally replace CrystalWeb. At this stage CrystalWorks has limited search capabilities, but it already has new and improved structure display and coordinate output features.

It is clear that there is already significant added value in the ability of CrystalWorks and associated tools to deliver structures from a variety of aggregated sources (commercial databases and open repositories). In particular CrystalWorks can generate a rich variety of different coordinate output file formats. Work, already completed demonstrates mechanisms for direct coupling to other tools such as DLV as developed within the CSE Department at Daresbury Laboratory.

Other groups are likely are to have their own specific needs. These include output of database structures in formats specifically tailored for input into a range of software packages. Please discuss this with your colleagues.

We believe it is important for us to get some idea of the actual size of the potential user base for these tools in the wider community.

We would like to open up discussionst on the current development potential for CrystalWorks.