Hi, I was trying to find information online/and in the archives of the mailing list to do what you are asking. You can try "help fit" which will give you some more commands to try. You can also try "help pair_fit". Unfortunately I know I'm doing something wrong so I can't get these commands to work properly without always returning an "ExecutiveRMS-error".
So for structure matching I exclusively use Chimera. Open your two structures, Tools->Homology->Matchmaker . The rest is self-explanatory. It will return an RMSD, has several algorithms and matching matrices to choose from, and will even show you the sequence alignment if you want. You can even interesting residues in the sequence alignment window and it will select them in realtime in the structure viewing window. Hope that helps, Sabuj Pattanayek yunbo.song wrote: > Ok, thanks. But, its not what I meant. I want to let 2 proteins > automatically overlap according to the amino acid sequence > alignment,i.e. the conserved residues can be overlapped. Can I do it use > pymol or any other program? > > thanks > May 5 > > > > hi, > > I had a similar question, and here is the answer. > > Jennifer, > > Yes.?Switch the mouse into "3 button editing mode", and then > shift-left-click-and-drag to rotate and shift-middle-click-and-drag to > translate. > > Cheers, > Warren > > I found that this approach works best if you are in stick or line mode. > I hope this helps. > > -Jennifer Pfingsten > (UCHSC) > > > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net on behalf of yunbo.song > Sent: Thu 5/5/2005 11:56 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] can superimpose two protein structures ? > > Hi, all, > > Can I use pymol to superimpose two protein structures ? How should I do? > If it cannot, anybody can tell me what program can do superposition very > easily? thanks! > > May 5 >
