Comparison of CA positions in two models allowing any order of fragments



Identify how many of the CA atoms in one model match CA atoms in another model. Separately identify how many of these go in the same direction and how many of the residue names match.


How chain_comparison works:

chain_comparison runs normally selects the unique part of the target model (the first model specified), then it takes the entire query model and counts how many residues in the target model are matched by a residue in the query model. If NCS is supplied, the unique part of the query is selected, NCS is applied and then the same analysis is carried out.

If desired, you can have chain_comparison write out all the residues in the query model that are matching residues in the target model.


Standard run of chain_comparison:

Running chain_comparison is easy. From the command-line you can type:

phenix.chain_comparison target.pdb query.pdb

If you want to compare P positions for RNA/DNA instead, you can say:

phenix.chain_comparison target.pdb query.pdb chain_type=RNA

Possible Problems

Specific limitations and problems:


Additional information

List of all available keywords