If you mean that you have many structure files for the same protein but with
different ligands you can automatically align them all based on just the target
site CA atoms (i.e. defined as those close to one of the ligands) using the
Job/Cocrystal superposition application in MIFit8
http://code.google.com/p/mifit/
See tutorial lesson 15. One of the outputs is a file containing all of the aligned
ligands.
It is also possible to perform bulk import of prealigned PDB files placed in the
same directory with the normal File/Open Models... command but holding down
the shift button and selecting the many structure files with the mouse.
Different models will be displayed in different colors.
For medically interesting proteins it is increasingly the case that there are
dozens of cocrystals in the PDB and it becomes tedious to understand how
they relate to each other without an alignment tool that can automatically run
over the whole set.
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