Dear Daniel
Thanks for the info. I knew that Brian Matthews' group had done some work
in this area.
Cheers
-- Ian
On 16 June 2014 11:16, Daniel Picot <daniel.pi...@ibpc.fr> wrote:
> Dear Ian,
> This has been discussed in a review and related articles by Brian
> Matthews and Liljun Liu:
>
> Matthews BW, Liu L. A review about nothing: are apolar cavities in proteins
> really empty? Protein Sci. 2009 Mar;18(3):494-502. doi: 10.1002/pro.61.
> Review.
> PubMed PMID: 19241368; PubMed Central PMCID: PMC2760356.
>
> Daniel
>
>
>
> Le 16/06/2014 11:32, Ian Tickle a écrit :
>
> Dear James
>
> You seem to be discounting the possibility of a true vacuum inside a
> structure, which is obviously not the same thing as 'something' (bulk
> solvent or whatever). I accept that this is unlikely in the case of ligand
> binding sites exposed to solvent, or indeed any site on the outer surface
> of the molecule, since any vacuum in that situation would be unstable
> against the ingress of water molecules, but it is possible in the case of
> fully-enclosed cavities (i.e. 'inner surface') that are normally
> inaccessible to water. I don't know if anyone has done a systematic survey
> of this, i.e. looking for cavities where the density appears to be actually
> zero (taking into account F000 of course), or at least significantly lower
> compared with the bulk solvent density (where the assumed value of F000
> wouldn't affect the result).
>
> Cheers
>
> -- Ian
>
>
> On 16 June 2014 07:37, James Holton <jmhol...@lbl.gov> wrote:
>
>>
>> Thank you Pavel for the clarification!
>>
>> What I was really trying to point out is that a "missing atom", occ=0.00
>> and occ=0.01 are not as similar as one might naiively think. Also, if you
>> put a ligand into a pocket and the occupancy refines to > 0, that does not
>> necessarily mean the ligand is "partially occupied". If the pocket is
>> actually filled with flat bulk solvent, then you expect the ligand
>> occupancy to be non-zero, simply because something is better than nothing.
>> However, if the bulk solvent mask were somehow "smarter" and filled the
>> pocket of a, say, 60% occupied ligand with flat bulk density at 40% the
>> level of bulk density used far away from any atoms, then one might actually
>> see the occupancy of a bogus ligand refine to zero. That is, a ligand
>> built into a pocket that is truly "empty" (filled with flat bulk solvent)
>> and then occupancy refined would actually be a "competition" between two
>> alternative hypotheses: 1) ligand in the pocket, 2) nothing but solvent in
>> the pocket. If the occupancy of the ligand refines to zero in this
>> context, then you can be quite confident that it didn't bind, at least not
>> in the given orientation.
>>
>> I fully realize that the implementation of this is easier said than done,
>> but perhaps it would be worth the effort?
>>
>> -James Holton
>> MAD Scientist
>>
>>
>> On 6/16/2014 3:04 PM, Pavel Afonine wrote:
>>
>> 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
>>>
>>>
>>>
>>
>>
>
>
