Thanks for the answer. Actually, it's the opposite. I have many structures that have different protein but with the same ligand(sugar). And I want to fixed the ligand and align the different proteins to see the active site.
On Sun, Apr 12, 2009 at 7:36 PM, John Badger <jbadg...@san.rr.com> wrote: > 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. > >
