Jie, The PyMolWiki can help you here!
First, the PyMol tricks, that you need, for aligning are described here http://www.pymolwiki.org/index.php/Intra_Rms But, if you already know what you want to align, the Kabsch algorithm can do the job (optimally well) http://www.pymolwiki.org/index.php/Kabsch (and it now works for Windows users, too). HTH, -- Jason On Tue, 2005-10-11 at 20:22 -0700, pymol-users-requ...@lists.sourceforge.net wrote: > Message: 4 > Date: Tue, 11 Oct 2005 10:48:25 -0700 > From: jy-ucsd <jiey...@ucsd.edu> > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] align selected regions > > Hi, all > I am trying to align two proteins, but I would like to specify > different > regions for different alignment, since the two proteins that I wish > to > align has a hinge region. > I tried the fit command, as the following: > fit (protein1 and chain A and resi 200-300 and name ca), (protein 2 > and > chain B and resi 200-300 and name ca) > > and it did not work, "no atoms selected". > > can someone tell me the best way to do it? > > Thank you > > Jie -- Jason Vertrees (javer...@utmb.edu) BSCB Graduate Student @ UTMB, Galveston http://www.bscb.utmb.edu :: BSCB @ UTMB http://best.utmb.edu :: B.E.S.T. @ UTMB http://pymolwiki.org :: PyMol Wiki
