Hi James,
a remark: different programs may treat occ=0 differently. In phenix.refine
(phenix.maps, etc) atoms with zero occupancy will be ignored for
bulk-solvent mask calculation, unless you ask to do otherwise. For example,
this means that if you want to calculate a ligand OMIT map both options
- removing the ligand from PDB file;
- setting its occupancy to zero and making sure mask does not ignore occ=0
atoms)
are a) not equivalent and b) both not good.
In first case (removing atoms from file) bulk-solvent will flatten residual
map (as you pointed out). In second case bulk-solvent will be excluded in a
very specific area, so that residual ("green") density you see there may be
either just bulk-solvent or ligand in question or a mixture; obviously not
a very useful information! This highlights the fundamental problem of flat
bulk-solvent model the way it's currently used.
Pavel
On Sun, Jun 15, 2014 at 3:01 PM, James Holton <jmhol...@lbl.gov> wrote:
>
> The principle difference between occ=0 and omitting the atom entirely is
> that occ=0 atoms exclude bulk solvent. Or at least they do for typical
> operation of contemporary refinement programs. So, by defining occ=0 you
> are forcing all map voxels within ~0.6A or so of your "invisible" atom to
> be vacuum. If you omit it, then the bulk solvent may "flood in", perhaps
> enough to pull the fo-fc peak down below 3x rms. How much the bulk solvent
> floods in depends on how nearby atoms exclude the bulk solvent, and this,
> in turn, depends on which refinement program you are using. Different bulk
> solvent implementations use different radii, "shrink" parameters, etc. In
> addition, bulk solvent always "bleeds" a bit into surrounding areas because
> the solvent B factor is never zero.
>
> The real problem, I think, is that for any voxel of the map there is
> ALWAYS "something there". The only question is: what is it? Is there a
> 100% occupied ligand? 100% occupied solvent? Two conformers of the
> ligand? Or is it some mixture of all these? If you are asking these
> questions I think it is most likely a mixture, and mixtures are hard to
> model. What is worse, mixtures of a partially-occupied ligand with bulk
> solvent taking up the slack is currently impossible to model. We will have
> to wait for partial-occupancy-bulk-solvent to be implemented before we can
> build representations of these alternative hypotheses and and test them
> with competitive occupancy refinement.
>
> The bulk solvent is actually a very good example of something for which we
> see "no evidence" in our electron density maps, yet we model it in because
> 1) we know it must be there, and 2) it makes our R factors lower. What
> more could you want?
>
> -James Holton
> MAD Scientist
>
>
> On 6/13/2014 7:45 PM, Frank von Delft wrote:
>
> Hi all - talking about ligands, a quick question on that old conundrum, of
> what to do about invisible atoms -- build them with occ=0, or omit them?
>
> For bits of protein, I know all the arguments; personally I prefer
> omitting atoms because:
>
> - for amino acid sidechains, their presence is implied in the residue
> name.
> - for whole residues, their presence is implied in the sequence
> numbering
>
> However: what about ligands? Nowhere else in the PDB file is their
> presence implied - or have I missed something?
>
> (Certainly disorder in a ligand is important information that needs to be
> captured!)
>
> Cheers
> phx
>
>
>
