Re: [Jmol-developers] CIF/mmCIF

[E.L. W. <eg...@sc...>]

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On Wednesday 24 March 2004 01:37, Miguel wrote:
> I have been looking at the CIFReader in cdk, with an eye towards sharing
> it with Jmol.
> I started looking at it because I thought it would be easier to do than
> CML, and I am hoping that Egon can help me with CML.
>
> Searching the web seems to reveal that the you spent a lot of your pre-CML
> days working on CIF/mmCIF.
>
> The 'CIFReader' in CDK is only a partial reader.=20

Correct. The CIF format is copyrighted (or even patented...) and you can ca=
ll=20
a reader a CIF reader if and only if it reads the *full* spec. The CDK read=
er=20
does not do that.=20

> Egon put in comments
> saying that it is ad hoc and only extracts some fields. It looks to me
> like it extracts:
>   1. cell data
>   2. atom coordinates
>   3. _symmetry_space_group_name_H-M
>
> Q: In the context of Jmol, would it be useful to have a reader that only
> supports these items?

It did not support more fields, because those were not used then... since J=
mol=20
can now display B-factor, occupency it makes sense to read those too...

> The PDB offically supports/promotes mmCIF. The .pdb reader in Jmol now
> extracts quite a bit of information from .pdb files.

Yes, it makes sense to read those fields from mmCIF too...

Egon

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eg...@sc...
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6

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