> The only difficulty I have with these movements is that when > you do fragment rotation you never know exactly what the axis > of rotation is going to be. Usually I have to play around > with the overall camera view and the atoms I'm grabbing a few > times before I can get the rotation I want.
I have received some good suggestions about how to deal with this, by having PyMOL automatically set the origin at the fragments center of mass. In the meantime, ctrl-shift-middle-click to set the origin on a particular atom before commencing to rotate. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ow...@lists.sourceforge.net > [mailto:pymol-users-ow...@lists.sourceforge.net] On Behalf Of > al_pie...@vrtx.com > Sent: Thursday, February 17, 2005 8:56 AM > To: Sri Krishna Subramanian > Cc: PyMOL-users@lists.sourceforge.net; > pymol-users-ad...@lists.sourceforge.net > Subject: Re: [PyMOL] Re: align proteins in pymol > > If you set the mouse mode to 3-button editing mode, you'll > see that Shift-Left and Shift-Middle are RotF and MovF, respectively. > > So with nothing selected, if you do Shift-Left, grab an atom > of a molecule and move it, the whole molecule will rotate > while all other structures are fixed. The same process with > Shift-Middle will translate that molecule only. > > If you only want to move part of a molecule, you can > basically break the molecule into 2 separate fragments with > Ctrl-Middle selections. Then when you do a rotation or > translation only the end of the molecule you grabbed will move. > > The only difficulty I have with these movements is that when > you do fragment rotation you never know exactly what the axis > of rotation is going to be. Usually I have to play around > with the overall camera view and the atoms I'm grabbing a few > times before I can get the rotation I want. > > > > Sri Krishna Subramanian <kris...@sdsc.edu> Sent by: > pymol-users-ad...@lists.sourceforge.net > 02/17/2005 11:35 AM > > To > > cc > <PyMOL-users@lists.sourceforge.net> > Subject > [PyMOL] Re: align proteins in pymol > > > > > > > Dear Torin, > Thanks for your reply. However my question > was not about automatic alignment of two protein structures. > I want to move one of the structures while keeping the other > one fixed, so that I can consider alternate alignments etc .. > So is there a way to do that with PyMOL. > thanks > krishna > > > align prot1////ca,prot2////ca > > > prot1 will then be superimposed onto prot2 > > > > your two proteins will obviously require some degree of homology. > > > > Best, > > Torin > > > > > > > > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide Read honest & > candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
