PDB Model/Structure Alignment

Align models in a PDB file or multiple structures in separate PDB files.

prody.apps.prody_apps.prody_align.prody_align(*pdbs, **kwargs)[source]

Align models in a PDB file or multiple structures in separate PDB files. By default, protein chains will be matched based on selected atoms and alignment will be performed based on matching residues. If non-protein atoms are selected and selected atoms match in multiple structures, they will be used for alignment.

Parameters:

  • pdbs – PDB identifier(s) or filename(s)

  • select – atom selection string, default is calpha, see Atom Selections

  • model – for NMR files, reference model index, default is 1

  • seqid – percent sequence identity, default is 90

  • overlap – percent sequence overlap, default is 90

  • prefix – prefix for output file, default is PDB filename

  • suffix – output filename suffix, default is _aligned