Steve, This is something PyMOL can do with a little help from Python... # PyMOL script: view2coord.pml
# get the current camera matrix v=cmd.get_view() # translate atoms to the current origin of rotation alter_state 1, all, \ (x,y,z) = (x-v[12],y-v[13],z-v[14]) # apply the rotation (matrix multiplication) alter_state 1, all, \ (x,y,z) = (x*v[0]+y*v[3]+z*v[6], \ x*v[1]+y*v[4]+z*v[7], x*v[2]+y*v[5]+z*v[8]) # end script After loading a molecule and choosing a view (either with the mouse, or using commands like "orient", "turn", "move", "center", etc.), you then simply run the script and save the new coordinates: load original_mol.pdb orient center 10/ca @view2coord.pml save transformed_mol.pdb quit Oh, and yes, PyMOL is still free unless you choose to pay for it. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-requ...@ccl.net] On Behalf Of Steve Bowlus > Sent: Wednesday, June 23, 2004 8:42 PM > To: chemis...@ccl.net > Subject: CCL:Orient molecule > > I am frantically searching for a simple piece of code that > will allow me to: > > Read a standard file (mol, pdb, Sybyl ...) select an atom to > put at the Cartesian origin select an atom to put on the X > axis select an atom to put in the XY plane Do a rigid > rotation Do sequential rigid rotations about Cartesian axes > Freeze the molecule in the new orientation Output the NEW, > transformed coordinates. > > This is equivalent to the Sybyl "orient" command, plus rigid > rotations, plus "Freeze molecule". But I have not found a > free (or even cheap) package that will freeze a molecule in > the new coordinates before output. > > Thanks in advance for any pointers, > Steve > > > -= This is automatically added to each message by the mailing > script =- To send e-mail to subscribers of CCL put the string > CCL: on your Subject: line and send your message to: > chemis...@ccl.net > > Send your subscription/unsubscription requests to: > chemistry-requ...@ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the > maintainer: > Jan Labanowski, jlaba...@nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > >
