I fully agree. Unfortunately, the perfect model does not exist (at least not
for protein crystal structures). It is like with Heisenbergs uncertainty
principle. Either one has a complete model with a number of atoms having a
coordinate uncertainty of 4-6 Å, or one has a model where the uncertainty of
all atoms is below say 0.5 Å, but with a lot of truncated side chains with
clearly contradict available biochemical evidence.
Cheers,
Herman
________________________________
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Gregory Bowman
Sent: Monday, March 26, 2012 4:17 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] REFMAC5 residues with bad geometry
But what about the issue of resolution? As was previously pointed out,
at say 3.2 Å resolution, many side chains will fail to fit, but it doesn't seem
appropriate to trim them all down. The users need to also be aware of the
quality/resolution of the structures that they are looking at.
Greg
On Mar 26, 2012, at 9:28 AM, Ed Pozharski wrote:
I agree with Eleanor 100%...
In my biased opinion, only the atoms supported by electron
density
should be included in deposited models. To satisfy the "but
this will
mess up the electrostatic potential coloring" argument (a valid
one, of
course), the "projected model" can be deposited alongside which
must be
clearly advertised as the unconstrained interpretation by the
structure's author.
Cheers,
Ed.
On Sun, 2012-03-25 at 08:36 +0100, Eleanor Dodson wrote:
As Garib says - an atom with occupancy 0.00 is treated
as a marker -
useful
for coot - but is not included in any X-ray refinement
at all.. Maybe
it
would be more aesthetic to maintain geometry but as
crystallographers
I
think we should be interested in the fit of model to
experiment -
right? -
and not in reporting a pseudo fit related to geometric
parameters
only..
--
Oh, suddenly throwing a giraffe into a volcano to make water is
crazy?
Julian, King of
Lemurs
--
Department of Biophysics
Johns Hopkins University
302 Jenkins Hall
3400 N. Charles St.
Baltimore, MD 21218
Phone: (410) 516-7850 (office)
Phone: (410) 516-3476 (lab)
gdbow...@jhu.edu
http://www.jhu.edu/bowmanlab
