This is a good point, the difference between Fo and Fc can be great if Fc is actually missing (an 'incomplete' structure). And of course this wreaks havok in defining the maskf for bulk solvent, and refinement, etc. Incomplete can be missing whole parts of the protein (say in model building) or it could mean looking for density of a surface-bound ligand (the recent discussion of masking out the suspect region is implemented in BUSTER and more recently, phenix's POLDER maps).
However, when it comes to the 'refinement' of incomplete structures, I've found that low resolution probability distributions for the missing atoms can improve the refinement and the resultant map via the 'MissingAtoms' channel of BUSTER-TNT during refinement[1]. There was also a phenix.refine use_statistical_model_for_missing_atoms from Tom Terwilliger, where the missing density is obtained from RESOLVE density modified maps. Of course, the best case scenario is to have an external source of phase information (say experimental phasing) and the incomplete Fc has less of an effect in the refinement and map quality. [1] Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2210-21. Epub 2004 Nov 26. Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Blanc E, Roversi P, Vonrhein C, Flensburg C, Lea SM, Bricogne G. Just my 0.02, F On Feb 21, 2017, at 4:53 PM, Hunter Moseley <hunter.mose...@gmail.com> wrote: > Is there a straight-forward way to estimate the amount of missing electron > density that a particular protein structure is missing based on the > difference between Fo and Fc? > > It appears that the normalization of the Fc due to the employing of a maximum > entropy method that keeps Fo and Fc comparable to the standard deviation of > Fo would make this difficult. > Or am I missing something? > > Cheers, > Hunter > > -- > Hunter Moseley, Ph.D. -- Univ. of Kentucky > Associate Professor, Dept. of Molec. & Cell. Biochemistry / Markey Cancer > Center > / Resource Center for Stable Isotope Resolved Metabolomics > Not just a scientist, but a fencer as well. > My foil is sharp, but my mind sharper still. > --------------------------------------------------------------- > Email: hunter.mose...@uky.edu (work) hunter.mose...@gmail.com (personal) > Phone: 859-218-2964 (office) 859-218-2965 (lab) 859-257-7715 (fax) > Web: http://bioinformatics.cesb.uky.edu/ > Address: CC434 Roach Building, 800 Rose Street, Lexington, KY 40536-0093 --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder ----------------------------------------------
