On Wednesday, 11 June, 2014 20:01:45 Gerard DVD Kleywegt wrote:
> > What you want is a test for how well each model agrees with its own map. It
> > is fair to argue that the model that is more self-consistent (agrees better
> > with its own map) is the better model. But you won't learn that by
> > comparing model A to map B.
>
> However, conversely, if your modified model fits the original map better than
> the model that was used to calculate the map itself, you've done a good bit
> of
> model building.
But the current context is a question about using EDSTATS, which asks for a
difference map as part of evaluating the fit.
If the fit of the original model is bad, its difference map is going to be
polluted by both positive and negative peaks. Any nearby residues
will get a bad score.
Now suppose you somehow have a new model that is perfect.
If you try to score the new model using that same map, those same
difference peaks are still present (obviously) and the nearby residues
in the new model will also get a bad score even though they are
blameless in that they wouldn't have generated any difference peaks
themselves, being "perfect".
So far as I can see, it never makes sense to score model A based
on a difference map generated from model B.
Ethan
> If you want to do this calculation (with all the warnings and
> caveats), you can also use MAPMAN -
> http://xray.bmc.uu.se/usf/mapman_man.html#S41 . The method you propose is
> essentially the same as this one: http://www.ncbi.nlm.nih.gov/pubmed/18598022
> but for a fragment of your macromolecule instead of for a ligand (if you
> don't
> have access to the journal, you can request a reprint here:
> http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=87 )
>
> --Gerard
>
> ******************************************************************
> Gerard J. Kleywegt
>
> http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
> Little known gastromathematical curiosity: let "z" be the
> radius and "a" the thickness of a pizza. Then the volume
> of that pizza is equal to pi*z*z*a !
> ******************************************************************
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
