Dont forget all the "atomic resolution" 3Å structures!
From: Pavel Afonine [pafon...@gmail.com]
Sent: Thursday, January 06, 2011 6:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance
accu
ariables (the single-bond torsion angles)"
> >
> >
> >
> > Overall this seems a reasonable claim.
> >
> > Colin
> >
> >
> >
> > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Charles W. Carter, Jr
> &g
Jr
> Sent: 06 January 2011 09:52
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance
> accuracies
>
>
>
>
>
>
>
> Begin forwarded message:
>
>
>
>
>
> From: "Charles W. Carter, J
Maybe if you are really into this, you could "go public" by writing a
letter to the editor (from the CCP4BB?), and I am sure there will be a
good response from the authors...
Jacob
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training
Behalf Of Charles
W. Carter, Jr
Sent: 06 January 2011 09:52
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies
Begin forwarded message:
From: "Charles W. Carter, Jr"
Date: January 6, 2011 10:51:20 AM GMT+01:00
Begin forwarded message:
> From: "Charles W. Carter, Jr"
> Date: January 6, 2011 10:51:20 AM GMT+01:00
> To: Gerard Bricogne
> Subject: Re: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies
>
> I echo Gérard's thought.
>
> Pascal Retailleau
Dear Axel,
On Sun, Dec 26, 2010 at 01:15:44PM -0800, Axel Brunger wrote:
> We defined "super-resolution" in our DEN paper as
> achieving coordinate accuracy better than the resolution
> limit d_min of the diffraction data. We proposed this
> definition in analogy to its use wide-spread use in
We defined "super-resolution" in our DEN paper as
achieving coordinate accuracy better than the resolution
limit d_min of the diffraction data. We proposed this
definition in analogy to its use wide-spread use in optical microscopy:
"super-resolution" methods such as STORM, PALM, and STED achi
gt; Sent: Friday, December 24, 2010 4:26 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Resolution and distance accuracies
>
> I have a program which computes the atomic electron density profile
> (attached) as you would see it in a map, using accurate scattering factors
> a
> I find the "super-resolution" claims in this paper a bit of a conjuring
trick.
I think it is understood that information cannot come from nothing. You
cannot cheat in basic physics. Interestingly, I had the same discussion with
bioinformatics colleagues a short time ago. The problem is the same
Sent: Friday, December 24, 2010 4:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution and distance accuracies
I have a program which computes the atomic electron density profile
(attached) as you would see it in a map, using accurate scattering factors
and taking the resolution limit
To get an idea about this signal:noise issue, I wonder what the B
factor of bulk solvent would be, if it is possible to think in such
terms, i.e., fill the bulk solvent with dummy waters and let the B's
do what they will. I wonder whether anyone has tried explicitly
modelling the whole unit cell th
I have a program which computes the atomic electron density profile
(attached) as you would see it in a map, using accurate scattering
factors and taking the resolution limit into account. I wouldn't call
the profile for a C atom with B=100 at 2.5 Ang resolution 'flat',
maybe 'flatter'. 'Flat' wo
Dear Gerard,
Actually, for some of the tests we turned off the DEN network restraints
for the last two refinement macrocycles, so, at least for these
particular cases, the DEN method truly found a better minimum
rather than forcing the system to the higher resolution structure.
Cheers,
Axel
O
Extrapolating to the infinite, I wonder how super-resolution fits into
MD models or structure predictions?
Jacob
On Thu, Dec 23, 2010 at 5:04 PM, Gerard Bricogne wrote:
> Dear Bernhard,
>
> I must say that I find the "super-resolution" claims in this paper a
> bit of a conjuring trick. If th
Dear Bernhard,
I must say that I find the "super-resolution" claims in this paper a
bit of a conjuring trick. If the final refined model has greater accuracy
than one would expect from the resolution of the data it has been refined
against, it is because that extra accuracy has been lifted fr
Re: [ccp4bb] Resolution and distance accuracies
Something related to the results in the 1984 paper, but never published, is
that the calculated electron density for an atom with a B of 100
Angstroms**2 is so flat that you wonder how those atoms can be seen in
electron density maps.
Ron
On Thu,
Oops I am outdated: Axel just emailed me that he describes an improved
coordinate estimate beyond the Rayleigh criterion in his recent paper
Schroder GF, Levitt M, & Brunger AT (2010) Super-resolution biomolecular
crystallography with low-resolution data. Nature 464(7292), 1218-1222.
For the defo
Something related to the results in the 1984 paper, but never published, is
that the calculated electron density for an atom with a B of 100 Angstroms**2
is so flat that you wonder how those atoms can be seen in electron density maps.
Ron
On Thu, 23 Dec 2010, Bernhard Rupp (Hofkristallrat a.D.
> can anyone point me to a more exact theory of distance accuracy compared
to
> optical resolution, preferably one that would apply to microscopy as well.
Stenkamp RE, & Jensen LH (1984) Resolution revisited: limit of detail in
electron density maps. Acta Crystallogr. A40(3), 251-254.
MX, BR
This posting concerning positional precision prompted me to recall a
CCP4 meeting (not a recent one) where a well-known crystallographer
(who shall remain nameless - present company excepted BTW - AFAIK the
crystallographer in question has never posted to this BB) claimed that
an atom with a B fact
Hi Nick
The 0.1 to 0.3 Ang range you quote obviously only applies to the kind
of atoms we as macromolecular crystallographers are interested in,
i.e. mostly carbon with some nitrogen & oxygen, and also at the
'typical' data resolution and B factors that we observe. For hydrogen
it would obviously
Dear Nick
I think the point here is more the precision achieved via the fitting
of atom positions according to the gradient of the electron density.
There is obviously an overall link of the detail of/in this gradient
to the measurable diffraction resolution, which can be estimated in a
number of w
We clearly have confidence in distance measurements in crystal
structures of an order of magnitude better than the resolution ie
0.1-0.3 Angstroms, but can anyone point me to a more exact theory of
distance accuracy compared to optical resolution, preferably one that
would apply to microscopy a
24 matches
Mail list logo
