Hi Dolev, The difference is that the menu action only aligns on C-alpha atoms. Since PyMOL 1.8 the menu label says “align > to molecule (*/CA)” to make this more obvious.
The exact command which is executed by the menu action is: align 4A11 & name CA & polymer, 3W15 & name CA & polymer, object=aln_4A11_to_3W15 The “polymer” selection makes sure that calcium atoms are not included, which also have name CA. See also: https://pymolwiki.org/index.php/Align Cheers, Thomas > On May 18, 2017, at 12:41 PM, do r <dolevra...@gmail.com> wrote: > > Hello > > I have noted that using action -> align -> to molecule via the GUI gives > (sometimes radically) different result then running align on the same > structures via command line. > > For examples, for PDB structures 4A11 and 3W15, the command > align 4A11,3W15, aligns 1632 atoms and gives an RMSD of 7.538, whereas > action -> align -> to molecule aligns 375 and gives an RMSD of 24.416. > I have also seen such differences on other pairs of structures. > > Any explanation of this phenomenon will be most appreciated. > > Thanks in advance > Dolev Rahat -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ 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
