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 ------------------------------------------------------------------------------ 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