It is often the case that one wishes a particular protein structure
to be the `parent' of the superimposition, i.e. the structure that
is un-transformed. Accordingly, the program PICKFRAME allows
one to select a particular reference frame for a particular domain
identifier. Given a transformation file and an identifier, the
program will set the selected identifier's transformation to the
unit matrix and zero vector, and transform the other structures
accordingly. This is useful if one wishes to combine different
transformation files (i.e. if a multidomain protein has
two domains, with each being similar to a separate domain).
The format is:
pickframe -f <transformation file> -i <domain identifier>
The output will be to the standard output (i.e. one need just
pipe the results into a file).
This program is very useful if one wishes to superimpose STAMP results for two different domains from the same protein. Since one can just make all transformations relative to the PDB file containing the two domains, and then combine the output into one transformation file.