Hi David, this is bug, indeed. I also hit this some time ago but didn't report it so far. The actual problem is that the cmd.super('1acb', '426d') fails completely and only aligns a single atom, resulting in a Null-matrix that collapses all of 1acb into a single point. The RMSD of 2.8 that you get in your last call is just an artefact that arises from aligning the correct protein to the collapsed one. Just run your example with GUI and you see what happens.
fetch 1acb fetch 426d copy 1acb_2, 1acb super 1acb, 426d super 1acb, 1acb_2, object=aln zoom aln I think the super command should check if the resulting matrix is orthonormal or at least not a Null-matrix. Cheers, Thomas On Wed, 2010-09-22 at 18:28 -0400, David Hall wrote: > In preparing my test for the odd request that I just sent, I came > across what seems to be a bug in super. It has to do with this weird > nucleic acid thing I was talking about. > > Here's the script this time: > from pymol import cmd > > cmd.fetch('1acb', async=0) > cmd.fetch('1acb', '1acb_2', async=0) > cmd.fetch('426d', async=0) > > > print "1acb_2"; print cmd.super('1acb', '1acb_2')[0] > print "426d"; print cmd.super('1acb', '426d')[0] > print "1acb_2_again"; print cmd.super('1acb', '1acb_2')[0] > > ~> ~/src/pymol_trunk_20100922/pymol -qrkc script2.py > PyMOL>run script2.py,main > 1acb_2 > 0.0 > 426d > 0.0 > 1acb_2_again > 2.80655193329 > > super should give an rms between 1acb and 1acb_2 of 0.0, which it does > at first. But once you super your protein to a nucleic acid that has > a calcium ion, when you run exactly the same command, you all of a > sudden get 2.8. Very weird... > > Note, this does not happen if you use 100d, which is a nucleic acid > without a calcium ion, does not happen if you use a pdb file with a > calcium ion, and does happen with 1d56, which is another nucleic acid > with a calcium ion I just pulled out. > > In pymol 1.2, it also behaved incorrectly: > ~> pymol -qrkc script2.py > PyMOL>run script2.py,main > 1acb_2 > 0.0 > 426d > nan > 1acb_2_again > nan > > > -David -- Thomas Holder Group of Steffen Schmidt Department of Biochemistry MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ 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