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RE: [ccp4bb]: How to deal with sidechainatoms with low electron density?
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Well, if crystallographers would deposit structure factors, then
very simple means of displaying local structure quality
like Real Space Correlation plots - proposed long ago
and again and again to no avail - would provide the user
with a clear assessment of the quality of the model in
whatever region one might be interested. It also would give the
depositor a valuable reality check and prevent much uncecessary
arguing later on. Even w/o the structure factors made available, a
real space correlation plot tells the user a lot more than the
(esentially redundant as it is in the PDB entry) infamous 'table 1'
of data collection and (global) refinement statistics...
A bit of prior discipline would be much better than much
posterior policing.
Cheers, BR
PS: Data, data, I need more data....for the puzzlers..
PPS: Advertisement: Read 'Homo Crystallographicus' in Structure.
------------------------------------
Bernhard Rupp
c/o
Dept. of Biochemistry and Biophysics
2128 Texas A&M University
College Station, TX 77843-2128
cell 925 209 7429
lab 979 862 7639
sec 979 862 7636
fax 801 880 3982
------------------------------------
> -----Original Message-----
> From: owner-ccp4bb@dl.ac.uk [mailto:owner-ccp4bb@dl.ac.uk] On
> Behalf Of fvan0987@itsa.ucsf.edu
> Sent: Friday, November 22, 2002 5:20 PM
> To: bhazes@ualberta.ca
> Cc: ccp4bb@dl.ac.uk; florian@cryst.bioc.cam.ac.uk
> Subject: Re: [ccp4bb]: How to deal with sidechainatoms with
> low electron density?
>
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> 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
>
>
> ----
> Filip Van Petegem
> University of California, San Francisco
> 513, Parnassus Avenue
> phone: 1-415-514-2836
> fax: 1-415-514-2550
> -----
>
>
>
>
>
>
> On Fri, 22 Nov 2002 09:58:04 -0700 (MST) Bart Hazes wrote:
>
> > *** For details on how to be removed from this list visit the **
> *
> > *** CCP4 home page http://www.ccp4.ac.uk ***
> >
> > 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
> >
> > ================================================
> ===============================
> >
> >
>
>