PdbTesting

From BioclipseWiki

Contents 1 PDB reading testing 1.1 Fails to read in CDK 1.2 Reads, but CDK lacks functionality 1.3 Reads, but connectivity messed up 1.4 Reads, but Jmol does not recognise secondary structure element 1.5 Works fine

PDB reading testing

The goal of this page is to examines the PDB reading and secundairy structure capabilities for the PDB files in the Jmol data repository. For the categories it lists the PDB identifier of examples for that category.

Fails to read in CDK

• 1HJE - opened with JCP
• 1CKV - practically too large to load

Reads, but CDK lacks functionality

Some things the CDK PDBReader simply cannot do.

• 1ALE - model info is not transported to Jmol
• 1PN8 - looks weird, might be OK

Reads, but connectivity messed up

Reads, but Jmol does not recognise secondary structure element

This means that the backbone is shown, and that 'select protein' is not empty. Not sure what goes wrong here. And verification with Jmol needs to be done; it might be a Jmol problem.

• 1CRN
• 1MBO
• 3OVO
• 1TOH

Works fine

• 114D
• 1B07
• 1BOQ
• 1D68
• 1EPL
• 1IHA
• 1PPA
• 233D
• 5CRO