Re: [ccp4bb]: How to deal with sidechainatoms with low electron density?

[<fvan0987@itsa.ucsf.edu>]

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Dear all,

It seems that every procedure used (lowering occupancies,
letting B-factor go up, cutting pieces from the residues...) each 
have their advantages and disadvantages.

The biggest problem is  the fact that everybody comes up with 
their own way of dealing with the problem, which may confuse 
people looking at PDB files.  Therefore, it would be much better 
if the PDB database would impose a number of rules about 
how to deal with residues with poor or missing densities, and 
not to give freedom to the crystallographer depositing the 
structure.  This is probably the only way of getting a 
standardized structure depostion rather than a mixture of clever 
ideas.

Filip


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Filip Van Petegem
University of California, San Francisco
513, Parnassus Avenue
phone: 1-415-514-2836
fax: 1-415-514-2550
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On Fri, 22 Nov 2002 09:58:04 -0700 (MST) Bart Hazes wrote:

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> 
> On Fri, 22 Nov 2002, Florian Schmitzberger wrote:
> 
> > Dear all,
> >
> > I was wondering what the most acceptable way to deal with 
(disordered)
> > sidechains/residues (e.g. sidechains of Arginines and 
Lysines) with very
> > low or no electron density is? Especially with respect to 
submission of
> > coordinates to the pdb-data bank.
> >
> > My initial approach was to set the occupancies of the atoms 
to 0
> and then
> > refine in Refmac. However I encountered that the geometry 
(bond lenghts
> > and angles) gets distorted between the atoms with normal 
occupancy
> and the
> > ones with zero occupancy. The other option to refine the 
residues as
> > alanines does not seem a very good idea to me, since it 
does not account
> > for something which is there, but strongly disordered. For 
me the most
> > ideal way to deal with them is to fix the B-factor to a very high 
value
> > and then refine with Refmac.
> >
> > What is the general opinion about this matter?
> 
> We have already heard a few "general opinions" which 
means that there 
> is not a
> clearly accepted code of best practise for this situation. I don't
> like either
> the 0.01 or 0.00 occupancy or high B-value solutions. In both 
cases
> the naive
> end user sees a sidechain in the model and will firmly believe 
that those
> atoms are exactly there and nowhere else. Of course it takes 
only a quick
> check of B-factor or occupancy to find out but I wonder how 
often that is
> done. I often don't even do that myself unless I have reason to 
be
> suspicious
> of a part of the structure.
> 
> The practise in my lab is to build what you see and to explicitly
> remove the
> atoms you don't see. So a lysine may have its beta and 
gamma atoms
> modeled but
> not the rest or a glutamate may lack its carboxylate. The 
residue
> name will of
> course still be the real amino acid at that place. Some 
programs may
> complain
> about incomplete residues but we don't have a problem with 
it. The
> best thing
> is, I hope, that a user will actually notice that there are atoms
> missing and
> therefore is alerted to the fact that these atoms are disordered
> (although we
> may have educate people that missing carboxylates can be 
due to radiation
> damage as well).
> 
> A different approach is to consider a structure as a model that
> accommodates
> both experimental data and basic protein geometry rules. 
When there
> is strong
> experimental evidence you build whatever the data supports 
even if that
> involves an unusual dihedral angle or so. When there is no 
data you build
> whatever molecular geometry dictate. In disordered regions 
where
> experimental
> data is weak one could thus build all common rotamers of a 
sidechain, 
> removing
> those that are clearly stericaly impossible and set all 
occupancies
> to zero.
> That should also really stand out to the user and, like the 
NMR
> world, we can
> claim to "see" dynamics for those regions where we really 
see
> nothing. It may
> even be possible to refine occupancies for the various 
rotamers if we 
> restrain
> or even constrain the atomic positions of the sidechain atoms 
(make
> them ride
> on on the mainchain atoms).
> 
> Bart
> 
> ================================================
===============================
> 
> Assistant Professor
> Dept. of Medical Microbiology & Immunology
> University of Alberta
> 1-15 Medical Sciences Building
> Edmonton, Alberta, T6G 2H7, Canada
> phone:	1-780-492-0042
> fax:	1-780-492-7521
> 
> ================================================
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> 
>