Dear Dale,

     There is perhaps a third factor in the progress you were able to make,
namely the improvement in the refinement programs. Your first results were
probably obtained with a least-squares-based program, while the more recent
would have come from maximum-likelihood-based ones. The difference lies in
the quality of the phase information produced from the model through
comparison of Fo and Fc, with much greater bias-correction capabilities in
the ML approach. Here, it removed the bias towards some regions being absent
in the model, and made them no longer be absent in the maps. So it is a
question of the quality of the phase information.


     With best wishes,
     
          Gerard.

--
On Tue, Apr 10, 2012 at 12:00:28PM -0700, Dale Tronrud wrote:
>    The phases do have effects all over the unit cell but that does not
> prevent them from constructively and destructively interfering with one
> another in particular locations.  Some years ago I refined a model of
> the bacteriochlorophyll containing protein to a 1.9 A data set when the
> sequence of that protein was unknown.  This is primarily a beta sheet
> protein and a number of the loops between the strands were disordered.
> Later the amino acid sequence was determined and I finished the refinement
> after building in these corrections.  The same data set was used, but
> a number of the loops had become "ordered".  While the earlier model
> (3BCL) had 357 amino acids the final model (4BCL) had 366.
> 
>    These nine amino acids didn't become ordered over the intervening
> years.  They were just as ordered when I was building w/o a sequence,
> it is just that I couldn't see how to build them based on the map's
> appearance.
> 
>    One possibility is that the density for these residues was weak
> and the noise (that was uniform over the entire map) obliterated their
> signal where it only obscured the stronger density.  Another possibility
> is that the better model had a better match of the low resolution F's
> and less intense ripples radiating from the surface of the molecule,
> resulting in things "sticking out" being less affected.
> 
>    Whatever the details, the density for these amino acids were too
> weak to model with the poorer model phases and became buildable with
> better phases.  The fact that they could not be seen in the early map
> was not an indication that they were "disordered".
> 
>    The first six amino acids of this protein have never been seen in
> any map, including the 1.3 A resolution model 3EOJ (which by all rights
> should have been called 5BCL ;-) ).  These residues appear to be truly
> disordered.  Going back to 3BCL - The map for this model is missing
> density for a number of residues of which we know some are disordered
> and some simply unmodelable because of the low quality of the phases.
> I don't know of a way, looking at that map alone, of deciding which
> is which.  Because of this observation I don't believe it is supportable
> to say "I don't see density for these atoms therefore they must be
> disordered."  Additional evidence is required.
> 
> Dale Tronrud
> 
> 
> 
> On 04/10/12 08:38, Tim Gruene wrote:
> > Dear Francis,
> > 
> > the phases calculated from the model affect the whole unit cell hence it
> > is more likely this is real(-space, local) disorder rather than poor
> > phases.
> > 
> > Regards,
> > Tim
> > 
> > P.S.: The author should not look at an 2fofc-map but a
> > sigma-A-weighted map to reduce model bias.
> > 
> > On 04/10/12 17:22, Francis E Reyes wrote:
> >> Hi all,
> > 
> >> Assume that the diffraction resolution is low (say 3.0A or worse)
> >> and the model (a high resolution homologue, from 2A xray data is 
> >> available) was docked into experimental phases (say 4A or worse)
> >> and extended to the 3.0A data using refinement (the high resolution
> >> model as a source of restraints). There are some conformational
> >> differences between the high resolution model and the target
> >> crystal.
> > 
> >> The author observes that in the 2fofc map at 3A, most of the model 
> >> shows reasonable density, but for a stretch of backbone the
> >> density is weak.
> > 
> >> Is the weakness of the density in this region because of disorder
> >> or bad model phases?
> > 
> > 
> >> Would love people's thoughts on this one,
> > 
> >> F
> > 
> > 
> >> --------------------------------------------- Francis E. Reyes
> >> M.Sc. 215 UCB University of Colorado at Boulder
> >