Jakob, Try,
rotate [xAxis, yAxis, zAxis], someAngle, yourSelection For example: # grab a protein fetch 1cll, async=0 # zoom & color zoom i. 20-25 color blue, i. 20-25 # rotate some selected atoms rotate [0.25, 0.4, 0], -12.5, i. 20-25 Cheers, -- Jason On Mon, Jun 28, 2010 at 11:14 AM, Jakob Nielsen <jtoudahl.niel...@gmail.com> wrote: > thanks, how can I flip a selection of atoms around an arbitrary axis? > > 2010/6/28 Edward A. Berry <ber...@upstate.edu> >> >> Jakob Nielsen wrote: >> > Dear Pymol users, >> > I would like to modify a protein pdb file with a "crankshaft" flip, >> > which is the anti-correlated double change: psi(i-1) += delta and phi(i) >> > -= delta. Such a change should leave the protein coordinates unchanged >> > effecting only atoms in residues i-1 and i. However implementation in >> > pymol (see below) changes the coordinates of _all_ residues from i-1 to >> > the C-terminal. >> >> I think this is expected because in general psi(i-1) and phi(i) >> will be rotating about different axes. You might try flipping >> the residue itself about an axis passing through its N and O atoms, >> followed by some regularization to fix the geometry. >> >> Ed >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
