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
