Hey Thomas, if you want to use align anyway, make sure to use the quite=0 option. The "quiet" option (if present) is set to zero by default for parsed PyMOL commands, but is not set for Python API calls.
align is nearly equal to cmd.align(quiet=0) Thus, if you want to get rmsd output, include quiet=0 and run your script with output redirection. Andreas On Thu, Oct 29, 2009 at 2:48 AM, Thomas Evangelidis <te8...@mbg.duth.gr> wrote: > Simple question, it must have been answered before but couldn't find > it so far: > > how can I get the RMSD value from the align command in a python > script? cmd.align() returnes a tuple of 8 numbers and none of them is > the actual RMSD value I get when I align these 2 structures manually. > > thanks,Tom > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > 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 > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ 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
