Highlights of biochemistry: molecular structures made visible

Highlights of Biochemistry

The plugin Chime is based on the ingeniously simple viewer RasMol. RasMol/RasWin was designed to handle single atomic coordinate files deposited in the PDB. Chime works on this as well. In some of the scripts presented in this project however I wanted to show more than is contained in a single PDB file. Therefore, the original PDB files had to be modified in varios ways according to purpose.

To demonstrate several states of a molecule deposited in separate PDB files I copy the coordinates into a single file and add corresponding chain identifiers (there may be a javascript workaround for the same task, but I may have to modify the PDBs for other reasons anyhow). The backdraw is a redundancy/overlapping in AtomNumbers which I am too lazy to change along. When different states (or homologous structures) were deposited by different authors, the orientation of the molecules may vary. Then they have to be aligned (e.g. with the swiss prot viewer) and the coordinates saved in the new orientation.

With very large multichain structures (as e.g. obtained from the EBI Protein Quaternary Structure server) there is a limitation in the PDB file format: there are not enough letters of the alphabet that Chime can discern. So chains to display have to be termed with single capital letters instead of lowercase or numbers. This does set a limit to the number of addressable chains.

Chime cannot display any linegraphics or alike by its own. So to display symmetry axes or other helping items I have to invent "molecules" whose coordinates are placed in the corresponding PDB files. These coordinates are not by the original depositors of the protein structure!

To display a bond between a protein and a ligand it doesn't suffice to have a CONECT record in the PDB file, the coordinates of the HETATM to show bonded have to be placed immediately after the corresponding amino acid record. In these instances I copy the record, generating redundancy in the file. Multiple bonds between atoms require additional entries in the CONECT records; if a bond is to be displayed in several modes, the corresponding atoms have to be given additional records with the same coordinates but different unique identifiers.

To speed transmission of the structure files, they are compressed (gzip). In some composite files records of items not demonstrated (e.g. water) are omitted. You may unzip and use the files, but be aware they may be adultered and contain information different from the original PDB files.

Impress  /  6-10-2004  /  Rolf Bergmann  /  http://www.papanatur.de/chimlime.htm