RE: [PyMOL] Iterative Magic Fit - Why not?

[Warren D. <wa...@de...>]

Shiven,=20
=20
"align" does indeed work just fine for 3hck and 2src...
=20
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?). =20
=20
The problem here is that members of the 3hck NMR ensemble are =
distributed randomly in space instead of being superimposed about a mean =
structure. =20
=20
To see this:
=20
set all_states, on
=20
To fix this:
=20
intra_fit 3hck
=20
Then, and only then, can you reasonably superimpose the 3hck ensemble =
onto the 2src crystal structure:
=20
align 3hck////ca, align 2src////ca
=20
Note that the align algorithm has been revised since 0.98.  For best =
results, use one of the latest beta versions:
=20
http://delsci.com/beta
=20
which have an "align" entry in the object and selection "action" menu.
=20
Another approach would be to specify that only state one source_state be =
used for the alignment:
=20
align 3hck////ca, align 2src////ca, source_state=3D1
=20
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?
=20
Cheers,
Warren
=20
________________________________

From: pym...@li... on behalf of Shivender =
Shandilya
Sent: Thu 12/15/2005 10:58 AM
To: pym...@li...
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!

Best,
Shiven


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