PDB files for Chime

A PDB file is what specifies the three-dimensional structure of a particular molecule you want Chime to display. It contains the X, Y, and Z coordinates for every atom in the molecule. You can get PDB files for many common small organic or biomolecules, as well as many proteins and nucleic acid structures.

PDB files are plain text, and for large molecules are rather bulky. This means they take a long time to transfer over the Internet. Therefore, Chime accepts PDB files compressed with gzip. The compressed files are renamed to type .pdb for technical reasons having to do with MIME types on web servers. Therefore, if you try to look at the contents of a PDB file and it looks like gibberish, you need to gunzip it first.

Gzip is free and is available for all common computer platforms. The gzip section of the FAQ explains how to use gzip.

(Gzipped PDB files cannot be used by RasMol unless they are first gunzipped.)


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