In : from credopymol import * # Fetch Both Structures from the database and load into PyMOL In : s1 = StructureAdaptor().fetchByPDB('2P33') In : s1.load() In : s2 = StructureAdaptor().fetchByPDB('3fv8') In : s2.load() # Align both chains with the PyMOL super command In : s1.Chains.align(s2.Chains) # Show contacts In : l1 = s1.Ligands In : l1.showContacts() In : l2 = s2.Ligands In : l2.showContacts() # Change to grid mode In : pymol.set('grid_mode',1)
A new version of the CREDO database has been released including 40,091 PDB structures. New features include:
For instructions on how to download and install the CREDO database, please go to the CREDO website.
the screenshot shows an example of how structures (chains) can be aligned including the interactions of their ligands with the help of the credoscript PyMOL interface. The structures are 2C5O and 2VTA respectively. The structures are represented in grid mode to view and rotate them both in parallel.
# Fetch all structures by UniProt accession In : structures = StructureAdaptor().fetchAllByUniProt('P53779') In : structures Out: [<Structure('1JNK')>, <Structure('1PMN')>, <Structure('1PMQ')>, <Structure('1PMU')>, <Structure('1PMV')>, <Structure('2B1P')>, <Structure('2EXC')>, <Structure('2O0U')>, <Structure('2O2U')>, <Structure('2OK1')>, <Structure('2P33')>, <Structure('2R9S')>, <Structure('2WAJ')>, <Structure('2ZDT')>, <Structure('2ZDU')>, <Structure('3CGF')>, <Structure('3CGO')>,
The CREDO database has been superseded by a newer version that encompasses the interactions between all residues. A website and RESTful web service to access the database has been developed as well and will be deployed soon.