Michael, Welcome to PyMOL! I don't think PyMOL is a replacement for SPDV -- the feature sets are distinct, and you should be able to use both together.
Yes, I think "align" is what you want. After... load x.pdb load y.pdb This would do an all-matched-atoms alignment: align x, y And this would do a CA-only alignment: align x////ca, y////ca To see which atoms are aligned, add and object name: align x////ca, y////ca, object=alignment Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Michael Bovee Sent: Friday, November 07, 2003 3:31 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] homologous alignments? Hi there, I'm switching to pymol from swiss pdb viewer because I simply needed better quality final images, but one of the coolest features of spdbv was the 'magic fit' where a single mouse click would superpose overall alignment of, say, the same protein from two different bacterial organisms (obviously high homology situation) opened in two different 'layers'. In pymol, it looks like the 'align' command is what I want (don't know if pymol uses the layers analogy), but I'm having difficulty understanding if I am to use parentheses and brackets as shown in the refman.pdf, and the use of this punctuation style doesnt seem to be defined in the pdf. USAGE align (source), (target) [,cutoff [,cycles [,gap [,extend \ [,skip [,object [,matrix [, quiet ]]]]]]]] (This style of outlining command formats is probably old hat to programmers, but that's not me.) So, is this the right command for superposition alignments in pymol, after loading pdb files x and y, for instance? Sorry for such a basic question; its getting late and I'm floundering :0) Thank you, --Michael
