Hi - a couple align questions:
1.  How do I get a listing of which atoms are used for alignment/RMSD calculation when aligning one molecule to another via the align to molecule pulldown (especially if they're different proteins)
2.  Is it possible to write an alignment script, e.g., align mol2 and (name n,c,ca) and (resid 10-64), mol1 and ...
where mol2 and mol1 are generic labels for the first, second, etc. molecules loaded?  I'm looking at NMR structure bundles where each conformer has a name from e.g., refined_1 to refined_16, and aligning each of them pairwise to the first in the set.  If I only load in a subset - say the 4 lowest energy, they may or may not include any given filename, so aligning them to an explicit name won't always work.
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016
Tel: 336 713-4194
Fax: 336 716-7671
email:  dhorita@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm