Analysis¶
Structural analysis tools: alignment, RMSD, clashes, pockets, and more.
Commands¶
/analysis align¶
Structural alignment of two objects.
/analysis super¶
Superimpose structures (more robust than align for low-homology).
/analysis cealign¶
CE-based structural alignment.
/analysis rmsd¶
Calculate RMSD between two selections.
/analysis clashes¶
Detect steric clashes.
/analysis pockets¶
Detect binding pockets.
/analysis loops¶
Identify loop regions.
/analysis sasa¶
Calculate solvent-accessible surface area.
/analysis fit¶
Fit two selections by atom pairs.
/analysis pairfit¶
Fit by explicit atom pairs.
/analysis binding_site¶
Identify binding site residues around a ligand.
/analysis fingerprint¶
Generate structural fingerprint.
/analysis morph¶
Create morphing trajectory between two conformations.
/analysis waters¶
Analyze structural water molecules.
/analysis ramachandran_plot¶
Generate Ramachandran plot.