Thank you Gerard for your suggestion. I will look into the paper you suggested and MAPMAN too.
I am "idealizing" fragments of PDB and while this would not agree when compared with the well refined structure, my goal really is seeing if these "ideal" fragments can still be identifiable when I look at the electron density and how to quantify that. (Ideal here refers to a small number of Phi and Psi values I picked as "representative" of different regions in the Ramachandran map). I picked on EDSTATS to explore since it gave individual residue information but realize now that since I am dealing with a small sub-set of residues an alternative is required. On Wed, Jun 11, 2014 at 2:01 PM, Gerard DVD Kleywegt <ger...@xray.bmc.uu.se> 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. 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 ! > ****************************************************************** >
