Hi, To complete the responses you already have got, I recommend to use LSQMAN ( http://xray.bmc.uu.se/usf/lsqman_man.html ) for your alignment task. It can only compare two structures at a time but LSQMAN can easily be run script-based (using one structure as the reference).
Select either all atoms 'at al' or define your own set with 'at de <atom definition(s) as in pdb> ' for the superimposition and choose the residue numbers of your ligand for alignment. Happy Eastern! christian rui wrote: > Hi, All > > I have dozens of complex structures ( protein + ligand ) and want to > align the structures based on the ligand. Does anyone know such kind of > program? Or if can get the information around the ligand site, that > would be even better. > Thanks. > > R -- _______________________________________________________________________ Dr. Christian Biertümpfel Laboratory of Molecular Biology NIDDK/National Institutes of Health phone: +1 301 402 4647 9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201 Bethesda, MD 20892-0580 USA _______________________________________________________________________
