CDS News - Crystallography Open Database [updated 17 Dec 2018]

The Crystallography Open Database (COD) is a collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers. The database is entirely open-access, with registered users able to contribute published and unpublished structures of small molecules and small to medium sized unit cell crystals to the database. Go to the COD Home Site for further details (use menu bar below).

The COD is available from the CDS/DL homepage via the CrystalWorks search and retrieval interface. No user registration is required to use this service.

CrystalWorks provides a full range of search facilities (author, journal, formula, compound name, etc) for the major crystallographic databases within a unified web browser interface. CrystalWorks also allows searching on atom coordination environment features.

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

Total number in Crystallography Open Database at the last count was 401,664
The Crystallography Open Database is updated daily
There were 18,813 new entries added over the year during 2017
There were 1,672 new entries added during January 2018
There were 1,154 new entries added during February 2018
There were 1,165 new entries added during March 2018
There were 826 new entries added during April 2018
There were 1,208 new entries added during May 2018
There were 1,096 new entries added during June 2018
There were 1,042 new entries added during July 2018
There were 842 new entries added during August 2018
There were 935 new entries added during September 2018
There were 968 new entries added during October 2018
There were 1,190 new entries added during November 2018
Statistics last updated 17/12/2018
Problem with display of COD structures containing Calcium

See details below:

Item added 19/07/18

COD entries display problem now fixed

A problem displaying COD structures containing Calcium was introduced with a recent upgrade. It is believed the error was created sometime late June. Under certain circumstances Calcium atoms were displayed as Carbon atoms in the JSmol display. The cause of the problem has now been identified and fixed.

Apologies for any inconvience caused. Entries from database other than the COD have not been affected

Item added 01/04/18

COD coordinate environment update

CrystalWorks searches on the coordination environment around a specified atom type (see Item added 05/10/15) has been updated for the Crystallography Open Database. This adds all entries to the end of March 2018 (the previous update was in Decmeber 2017).

Item added 13/10/17

The COD update problems have been resolved

Item added 12/10/17

The COD update failed this morning

The daily update of the Crystallography Open Database failed this morning because a disk partition was filled. We have restored the update from 11/10/17 pending the disk partition size being increased.

Please note that any searches between 4:30 and 9:00 BST would have yielded no COD entries. Please repeat any searches peformed during this period.

Item added 14/05/17

The transfer to the new server has been successful

The move to the new server was on 10/05/17. Users may have experienced problems in the period immediately after the transfer. All technical issues now seem to be fixed.

If you experience any continuing problems contact cdsbb@stfc.ac.uk

Item added 01/08/17

Problem with display of COD search results now fixed

There has been a problem with display of results obtained from searching using the the CrystalWorks open access COD option. The problem was introduced with modifications made at ~11:00 BST and lasted for about 2 hours. It has now been fixed. Please repeat any searches made.

Item added 15/03/16

More on annotations

The list of allowed characters that can be used in annotations (see Items added 26/02/16 & 27/02/16) has been extended. In addition to the set of alphanumeric characters you can include any characters from: -.():~

The comma is used as a separator between COD entries. The "~" character is render as the comma character in the text displayed by CrystalWorks. The "!" character is rendered as "/".

Item added 27/02/16

You can now add annotations

It is now possible add annotations to your Hits list. The link below illustrates how this is done:

http://cds.dl.ac.uk/cgi-bin/rfm/trawl?9000580_Armalcolite+from+the+moon,9012889_Pyroxferroite+from+the+moon

Please note that only alphanumeric characters are allow in any annotation strings - indicate spaces using the "+" character. Define the start of the string with "_".

Item added 26/02/16

Define a CrystalWorks Hits Set of COD entries via a URL

Searching the Crystallography Open Database is already freely available using CrystalWorks via the CDS/DL server, and you do not need to register for a username. When you have selected a list of COD entries of interest it is now possible to share them with your colleagues or a wider community by defining a specific URL.

For instance the URL link given below will launch a Crystalworks session with a Hits set comprising the COD entries 9000580 & 9012889.

http://cds.dl.ac.uk/cgi-bin/rfm/trawl?9000580,9012889

The syntax is quite simple and it is easy to see how to change and add further entries.

This system is under development, but you are welcome to generate URLs for your own Hits sets. These can be added to our own webpages, included in emails or used in social media postings, etc.

Item added 20/01/16

A problem with the cctx site is now fixed

CrystalWorks generates structure display from the information in CIF files provided by the Crystallography Open Database. In most cases symmetry operators are given explicitly, but in a few cases only the Hall symbols is provided. In those instances CrystalWorks looks up the information on the fly by accessing the Lawrence Berkeley National Laboratory web service at:

http://cci.lbl.gov/cctbx/explore_symmetry.html

Lawence Berkley recently introduced a bug for Hall including the " symbol. This has been reported and is now fixed. The problem was first identified the calcite entry, COD 2100992.

If you suspect a reocurrence of similar problems please check the corresponding CIF file.

Item added 05/10/15

COD entries now searchable on coordination environment

CrystalWorks searches on the coordination environment around a specified atom type has now been implemented for the Crystallography Open Database. This brings it into line with the Cambridge, ICSD and CrystMet databases.

This option for the COD has been implemented for both the ClassicPlus (username required) and COD (fully open access) versions of CrystalWork. It is also implemented in the version of CrystalWorks accessed via the RSC NCDS portal.

The files processed to allow COD coordinate searching were downloaded 30/09/15. Daily processing is not currently implement for this search option, but we hope to have this in place shortly.

Please note that search files are generated from the raw atom coordinate information. Disordered structures may sometimes cause problems, and this may ocassionally result in false hits or some being missed. You can usually check for such problems when you use the structure display submenu when you review your Hits List.

Item added 07/09/15

The number of COD entries now exceeds 1/3 million

The number of Crystallography Open Database entries has now reached 334,152. It has been rising at an average of over 100 entries per day over the last four weeks.

Item added 12/05/15

Daily addition of COD data updates to CrystalWorks now in place

Daily data updating from the main Crystallography Open Database server in Lithuania has been in place for a while and is working reliably.

Processing of these data updates has now been automated, and this process is also performed daily. Updated data is loaded to both the CrystalWorks COD version (freely available to all) and to the CrystalWorks "classic" plus COD version (CDS/DL username required). Both CrystalWorks options can be accessed via the CrystalWorks header near the top left on the CDS/DL homepage.

The job to download updates from the main COD server is currently launched at 3am every morning. Processing of the updates for CrystalWorks use is launched at 5am and the process completes ~5.30am.

Updating of listed update information is currently performed manually - exact details may be a little out of date. The update process is still being refined. Please report any problems you may encounter to cdsbb@stfc.ac.uk.

Item added 13/04/15

Daily data transfer has been implemented for COD

Data updating has now been upgraded for the Crystallography Open Database, and automatic data transfers have been implemented. The very latest data sets and any corrections available on the central COD website are now downloaded to the CDS/DL server daily.

Until now our prototype CrystalWorks system (see Items added 21/10/14 & 18/3/15) for the COD database used data downloaded from the main COD website in July 2014.

The COD data now available was downloaded and processed for use via CrystalWorks today and will be kept current. In addition we have corrected a number of errors and data omissions which were introduced during the data format conversion process required in loading into CrystalWorks.

There is still some work to be done on automating the format conversion and data loading process. However, is intended to implement weekly (or possibly daily) updates for COD via CrystalWorks.

Item added 18/03/15

There is a new implementation including COD together with the "classic" databases

There is a new development for CrystalWorks which allows searching over the "classic" databases (CSD,ICSD,CRYSTMET & CDIF) as well as the Crystallography Open Database (COD).

The total number of searchable entries included this expanded combined database collection is now 1,175,211. A link to the expanded collection including COD has been added to the CrystalWorks header on the CDS/DL homepage.

You need a CDS/DL username to access the combined or classic system. A username is not required to search the COD system by itself. The Coordinate environment search option has not as yet been implemented for the COD entries.

Please try out the new system and report back any problems.

Item added 22/11/14

New links added to pulldown menus

Links to Crystallography Open Database (COD) searching using CrystalWorks and the links example page (see Item added 21/10/14) have been added to the CrystalWorks header on the CDS/DL homepage.

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 Crystallography 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.