"align" does indeed work just fine for 3hck and 2src...
3hck is an NMR structure ensemble, and PyMOL superimposes ensembles based on their average ensemble coordinates, not based on just one arbitrary structure (as is perhaps the case with DeepView?).  
The problem here is that members of the 3hck NMR ensemble are distributed randomly in space instead of being superimposed about a mean structure. 
To see this:
set all_states, on
To fix this:
intra_fit 3hck
Then, and only then, can you reasonably superimpose the 3hck ensemble onto the 2src crystal structure:
align 3hck////ca, align 2src////ca
Note that the align algorithm has been revised since 0.98.  For best results, use one of the latest beta versions:
which have an "align" entry in the object and selection "action" menu.
Another approach would be to specify that only state one source_state be used for the alignment:
align 3hck////ca, align 2src////ca, source_state=1
Regarding your comments, I would be surprised if DeepView magic fit owned PyMOL "align" in the general case -- but if it does, then by all means, please use the better product.  No one has ever forced a Troll to use "pathetic" software when there are such "fantastic" and "intelligent" alternatives available...but for some reason, they just do.  Pretty strange, eh?

From: on behalf of Shivender Shandilya
Sent: Thu 12/15/2005 10:58 AM
Subject: [PyMOL] Iterative Magic Fit - Why not?

Hi All,

Is there any possibility that Pymol may have the ability to "intelligently" superimpose two(or more) structures, without requiring the user to fiddle with selecting exactly the same number of atoms/residues. The "align" command fails pathetically in many instances, case in point, try aligning (or fitting) 3HCK and 2SRC.

In this scenario, DeepView (Swiss PDB Viewer) excels fantastically. Just select "Magic Fit" or "Iterative Magic Fit" from the "Fit" menu, then select the structures and alignment level from a simple drop down menu and viola! I wonder how they do it. (And lament that DeepView is no longer being developed).

Apologies for sounding so trollish!


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