Hi Francis, Once I had asked Pavel Afonine the same questions and these were his suggestions but most of these can be implemented in phenix...
I guess there is no general/unified procedure to do this, and in most of cases the tools and outcomes vary case by case. Some general points: - Removing parts of model is unlikely to improve the map simply because this makes model even more incomplete. The main purpose of computing the omit map is not to improve the overall map but to verify the atoms in question. - Typically, the density appears weak because the signal is buried in noise. For example, we do not see H atoms in 2A resolution maps not because the information about them is not there (note, H atoms being weak scatterers contribute the most to low resolution reflections - similarly to bulk solvent, and their contribution to high resolution data approaches zero), but because the model quality and therefore noise at that resolution such that it hides hydrogens' signal. However, we do see H atoms at high resolution (say 1A and higher) not because of presence of high resolution reflections, but because the model quality is typically high and the noise level is below the hydrogens' signal. Having said this, one possible way of improving your "weak density" is to improve the model as much as you can: make sure you modeled all alternative conformations, all solvent, etc. - B-factor sharpening may help, although keep in mind that it will enhance the noise too. - Other options: kick maps, omit kick maps, b-factor sharpened kick maps... - You can try GrowDensity method (Acta Cryst. (1997). D53, 540-543) which is available as phenix.grow_density. This is still under (slow) development, so if you decide to go this route than I can help you with the details. Pavel. HTH, Shya On Tue, Aug 23, 2011 at 2:36 PM, Francis E Reyes <francis.re...@colorado.edu > wrote: > Seems to be a quiet day on the BB, so I propose this question: > > > Suppose you have a ligand in the binding pocket and some mediocre data (3 A > or so), the 'core' of the ligand is well defined in 2Fo-Fc map using the > model phases of your protein, however there are 'chains/tails' of the ligand > which are not. Composite omit or simulated annealing omit maps do not > produce density for these 'chains' > > The question here is how the chains/tails should be modeled (if at all). > > > [1] Model in the core, but remove the atoms for the chains (and conclude > the diffraction data do not support interactions with the protein and > subsequent experiments are needed (higher resolution data, biochemical data, > etc)). > > or > > [2] Model in the chains/tails noting that potential hydrogen bond > donors/acceptors on the protein are within hydrogen bonding distance to the > chains/tails. You do this and subsequent refinement still does not produce > the expected density for the chains. > > > or > > [3] Your solution here. > > > > If this situation has been discussed before, please let me know . > > F > > --------------------------------------------- > Francis E. Reyes M.Sc. > 215 UCB > University of Colorado at Boulder >
