PDB Index

If you have set your mime types to include chemical/x-pdb and set the extension for this as .pdb, then any of the following examples can be downloaded as their atomic coordinates in PDB (Brookhaven Protein Database format) or MOL (Molecular Design Ltd) file format and automatically parsed to RASMOL or viewed with the MDL plugin CHIME.

RASMOL, vs 2.6, which runs under Windows (Win 3.1 Win95 or WinNT), MAC and UNIX is available from Edinburgh or from the RASMOL pages at UMASS, Amherst.

The University of California, Berkeley have created a modified version that can open several files and move molecules around independently.

If you don't see a rotating molecule of Viagra below this line then you will need to install a plug-in for Netscape or Internet Explorer from Molecular Design Limited, Information Systems, Inc. (MDL). MDL used over 10,000 lines from RASMOL in creating CHIME and have provided a version free for academic and non-commercial use.

If you do, then to change the settings, left click on the MDL logo, or right click on the display to bring up the menu options.

Viagra - sildenafil citrate (citrate not shown)

Select to highlight the benzene ring. Select to revert to the original display.

• trans-[Rh(py)4Cl2]Cl.5H2O Gillard's Compound
• C60
• FeTPP
• Capsaicin
• Cisplatin (anti-cancer reagent)
• erythromycin C I had a bout of bronchitis in February!
• Hexol
• Limonene
• ZrTPP2
• [CoEDTA]-
• trans-[Co(en)2Cl2]+
• D-[Co(en)3]3+
• Co(salophen) reacted with Sulfur
• Caffeine
• Eugenol
• Fenfluramine
• Phentermine
• Vanillin
  This is only a selection of the numerous PDB files held at this site, to see others, try a search using pdb as the search term or try out the database arrangement using Chime and Rasmol scripts and JAVA.

If you are interested in the structures of proteins, then you should check out the excellent arrangement called Molecules R US for viewing files in the Brookhaven Protein Database.

Cn3D is available from NIH and although it does not read a PDB (it uses ASN.1 which is more compressed than PDB) it will write a PDB as output. You will need to set your MIME type to chemical/ncbi-asn1-binary.
Another source of PDB files is the Department of Chemistry, Okanagan University College, especially Natural Products.

Created Sept 1996. Last modified 6th May-98.
URL http://wwwchem.uwimona.edu.jm:1104/spectra/pdbIndex.html