Python-based
Hierarchical
ENvironment
for
Integrated
Xtallography
The purpose of analyze_alt_conf is to analyze alternative conformations (focusing on side-chains) for a structure and an optional comparison structure.
The problem that it solves is that if you have multiple conformations present in two structures, identifying which ones match and which ones are unique is tedious.
This tool first superposes all models that are supplied. Then it analyzes the unique residue conformations in each model that is supplied. Residues that superpose with an rmsd of min_rotamer_rmsd (default of 0.25 A) or better are considered the same conformer; those with a larger rmsd are considered different.
If there are two models supplied, the tool then compares the unique conformers in the first and second models. It identifies which altlocs in the first model (m1) match which altlocs in the second model (m2), and which are unique in one model or the other.
Running analyze_alt_conf is easy. From the command-line you can type:
phenix.analyze_alt_conf model.pdb other_model.pdb
where model.pdb is the model you would like to use as a starting point and other_model.pdb is an optional comparison model.
The procedure only analyzes alternative side-chain conformers, not main-chain. If you main chain has substantial alternative conformations (not just slight adjustments to match the side chain conformers), you will need to use another approach.