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Generating a set of superimposed structues

The TRANSFORM program included in the STAMP package can be used to generate sets of superimposed structures from the output of a STAMP multiple alignment run. For example, the output from the multiple alignment in the previous section can be fed into TRANSFORM as follows:

transform -f ac_prot.9 -g -o ac_prot.pdb

This will read in the files, transform the coordinates and save them to the file ac_prot.pdb (with each chain labelled starting with a different letter).