CrystalEye - Re: a csd alternative

I replied to Michael/Proclus on a different hread before I read BO as 
follows: This might as well act as a pre-formal announcement for 
CrystalEye. We see this as a rich source of accurate fragments for 3D 
molecular building

Michael,
This has come my way through CCP4BB.

You are welcome to the coordinates from WWMM as long as you 
acknowledge source. It was slightly pre-CC licenses but they should 
impicitly carry CC-BY. The WWMM molecules are slightly difficult to 
extract en masse as the metadata are fully exposed by require a link 
to the data so you have to write a simple script. This was not 
anticipated when we first put them in.

You may also be interested in http://wwmm.ch.cam.ac.uk/crystaleye 
which aggregates structures from the current crystallographic 
literature with complete metadata. There is a also a 2D image 
autogenerated by CDK. You mention "image" - I suspect you mean 3D 
image but 2D are also important. We shall be extracting ca 30K 
structures/year in this way and we have a significant back archive.

We would hesitate to use the term "CSD alternative" for CrystalEye - 
it does things that CSD does not do and vice versa. For example it is 
not comprehensive, but it is Open and creates/allows derivative works.

We expect to create a search interface fairly soon probably based on RDF.

P.



At 19:12 18/05/2007, proclus-x7PKJuapCgi0fEd0lbWiZA@xxxxxxxxxxxxxxxx wrote:
> On 18 May, Rajarshi Guha wrote:
> > Will these be 2D structure diagrams? Or ray traced 3D images? If the
> > former what is the need to store these? They could be easily
> > generated on the fly (either by local software or by web services
> > such as  http://rguha.ath.cx:8080/cdkws/services/StructureDiagram?
> > wsdl). If the latter, what is the utility of static 3D images (apart
> > from the eye-candy aspect)
>
> Quick access in the browser window is the answer, accessible to anyone
> without special configuration.  I haven't decided on line v. rendered
> diagrams.  Maybe both.
>
> > You can get 3D coordinates for most of PubChem from http://
> > www.chembiogrid.org/cheminfo/p3d - depending on the mode of access
> > (such as bulk downloads) you can get access to the underlying
> > database if needed.
>
> Thanks for the suggestions!
>
> Regards,
> Michael L. Love
>
> > -------------------------------------------------------------------
> > Rajarshi Guha  <rguha-GZvvpLG7cYSVc3sceRu5cw@xxxxxxxxxxxxxxxx>
> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04  06F7 1BB9 E634 9B87 56EE
> > -------------------------------------------------------------------
> > A sine curve goes off to infinity, or at least the end
> > of the blackboard.
> >       -- Prof. Steiner
> >
>
> --
> Visit proclus realm! http://proclus.tripod.com/
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Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road,  Cambridge CB2 1EW, UK
+44-1223-763069