I agree, what are the exact criteria for fitting in pymol? Currently i'm using SwissPDB viewer for quick fitting as this is pretty robust and usually comes up with something sensible. This is satisfactory for viewing but saving a swiss pdb fit for use in pymol is not. Pymol still seems to have problems with anything but the easiest fits when using the align command.
One further related question- how do you pick different models from and NMR ensemble and align them all to the best fit? cheers Jules On Wed, 19 Feb 2003, Michael Ford wrote: > I know it seems like every other question is on this subject but..... > > I saw from an earlier message the following statement from Dr. DeLano > > > PyMOL's fitting abilities are improving: the upcoming version (v0.80) > will have the ability to do an on-the-fly sequence-alignment followed by > an optimized structure alignment, saving considerable time and hassle. > > > > Has this been implemented (I'm running the latest version 0.86) > > I have 2 proteins that are identical, but for reasons of no great interest, > have > different numbering schemes. I have the documentation on the align command, > but > it doesn't work (malformed selection) > > Any help is appreciated..... > > Mike Ford >
