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