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Sorry for sounding terse, but I think this discussion completely
misses the point.
The real problem is the unreasonable assumption that
a careless, ill-prepared user or an automated piece of
software could grab a structure out of the
PDB, and obtain meaningful functional insights that depend on
the detailed geometry of individual sidechains
– AS LONG AS WE HAVE A CONVENTION FOR REPORTING DISORDERED
SIDE CHAINS.
I think this whole discussion is base on two fallacies:
FALLACY 1
A crystal structure, as long as the x,y,z and B for
all atoms were determine by refinement, will
allow a careless/unprepared user to extract meaningful functional
information.
The usefulness of a crystal structure
to a careless or ill-prepared "user" is not limited by
the fact that they might mistake a truncated lysine for an alanine.
Instead, the carelessness and lack of preparation that
lead to this particular mistake also lead to a myriad of
other, equally bad mistakes.
FALLACY 2
The x,y,z, B model determined by a crystal structure accurately
captures
the structure and dynamics of a protein.
Crystal structures, while they are the best we can
do, are inherently poor descriptions of the extremely complex
conformational
variability and structural dynamics that give proteins their
interesting properties.
This is why our Rfree typically hovers around
25% while the Rmerge is at 3-5%. Rfree and Rcryst are
high not due to the inaccuracy of our data, but due
to the "inadequacy" or our models.
Details of a final crystal structure, particularly in areas with
marginal density, are also
the result of many ad hoc decisions. One persons alternate conformer,
is another person's noise.
So, lets focus our energy on educating potential end users on how
crystal
structures are determined and what information one can extract from them
with what level of confidence.
I hope I did not piss off too many people with this email.
Cheers,
Ulrich
On Jan 10, 2007, at 12:18 PM, Thomas Stout wrote:
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It seems to me that the best solution here would be to model what is
actually going on: disorder. For the example of a lysine where
there is
limited or poor electron density beyond the C-beta, the best
representation of the physical model would be an ensemble of all
possible rotamers of what is physically present in the crystal.
Having
"N" sidechains (alternate conformers) with occupancies of 1/N would be
extremely clear to all users (novice and expert alike) as well as most
if not all software.
-Tom
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of
Anastassis Perrakis
Sent: Wednesday, January 10, 2007 7:47 AM
To: CCP4 Board
Subject: Re: [ccp4bb]: Modelling disordered side-chains
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My two cents and a summary:
1. omitting the atoms on a clearly indicated LYS residue is a choice.
It creates a striking phenotype and does not mislead. It might however
cause trouble in 'user' analysis software that will not like LYS
without
its atoms. Plus, we know for sure that these atoms are there, so we
omit
them ...
2. modeling the lys in a common rotamer is also a legitimate choice,
since B's will inflate. But, indeed thats not obvious when you look at
the structure. Also, most unfortunately most analysis software and
users
will ignore B's.
3. putting occupancy to 0.0 does not look like a good choice to me.
the atoms still show on display and no user or software uses
occupancies
any more than B factors, so to me it combines all the trouble
together.
on top, some refinement programs when occ is 0, they might switch off
geometric restraints including VdW repulsion and then its a real mess.
i still hesitate between 1 and 2, but my current choice is to use 2
(let
B's inflate) and i admit i have limited sympathy for PDB users that
ignore B values and also cant be bothered to use the EDS (i.e. i
ignore
the problem, which is not very nice, but ...)
Tassos
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