Multiple Template Alignment: structalign

You can specify the input as multiple files in PDB format, or as a Maestro file. The templates should consist of single chains. To use the output files, each must be imported into Find Homologs and selected as one of the templates, replacing the original, unaligned version.

This utility can be used to structurally align a set of proteins to a reference. The syntax is:

structalign [options] reference-file input-files

The reference file and the input files can be in PDB or Maestro format. You can use a single multi-structure Maestro file rather than a set of files with a single structure in each. The output file name is generated by adding the prefix rot- to the input file name. For a description of the options, run the command with the -h option.

If any of the templates have multiple chains, use the getpdb utility (see Extracting Proteins from the PDB: getpdb manual) to extract each chain into a separate .pdb file, then run structalign again.