Re: [ccp4bb] poll: cutoff for "high resolution"

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: poll: cutoff for "high resolution"
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-05-15

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From: "V {- dot -} Nagarajan" tatoosh {- at -} GMAIL {- dot -} COM
Date: 2008-05-15

Subject: Re: poll: cutoff for "high resolution"
From: Ed Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2008-05-15

Sure, it has very little to do with original question about what
constitutes "high" resolution. And that term is quite relative. 1.8A
data is definitely of higher resolution than 2A, but is it "high"? (Not
to mention the issue of subjective choice of resolution cutoff). The
only way to define these terms is by looking at what is the average
resolution in the PDB, and then calling top 25% "high resolution".
Perhaps PDB should recalculate this magic number with every release, so
that we know what to do (:-) Then, of course, we will have to devise a
sliding scale based on resolution, molecule type (aren't protein-DNA
complexes on average lower resolution?), etc. We'll call this new field
of science resolutionomics.

You (and many others) are also quite right that there is a difference
between resolution and optical resolution. My quite primitive
understanding of it is that you should be able to see local minimum
between two peaks to be able to "resolve" them. It appears that
hydrogen still retains enough electron density (at least in water)
http://academic.reed.edu/chemistry/roco/Density/images/water_rho_relief_large.jpg
to form real peaks. If, however, these peaks are watered down by atomic
motions, then perhaps hydrogens sometimes could not be "resolved" at
all, and thus they are indeed "less equal". I was just trying to
protect poor creatures, after all they only got one electron to hold on
to (:-)

Ed.

On Thu, 2008-05-15 at 11:40 -0700, William Scott wrote:
> The electrons on the hydrogens won't be centered about the proton
> nucleus, so if you want to resolve that as anything more than a bump,
> you will need a lot better than 1 Ã… (or neutrons). But in fairness
> the original question asked what you can call "high" resolution, not
> what you can call atomic resolution. I think anything better than ~3
> Ã… should allow unambiguous definition of nucleotide and amino acid
> positions.
>
>
> On May 15, 2008, at 11:28 AM, Ed Pozharski wrote:
>
> > Of course. However, C=0 bond is ~1.2A, and bonds made by those pesky
> > hydrogens are ~1A. And I would think (it is semantics again) that to
> > reach atomic resolution you have to resolve all atoms, otherwise
> >
> > "All atoms are equal, but some (non-hydrogens) are more equal than
> > others."
> >
> > Cheers,
> >
> > Ed.
> >
> > On Thu, 2008-05-15 at 10:08 -0700, William Scott wrote:
> >> On May 15, 2008, at 10:01 AM, Ed Pozharski wrote:
> >>
> >>> 1.2A (not surprisingly since this is about the length of covalent
> >>> bond).
> >>
> >> A carbon-carbon single bond is about 1.55 Ã….
> > --
> > Edwin Pozharski, PhD, Assistant Professor
> > University of Maryland, Baltimore
> > ----------------------------------------------
> > When the Way is forgotten duty and justice appear;
> > Then knowledge and wisdom are born along with hypocrisy.
> > When harmonious relationships dissolve then respect and devotion
> > arise;
> > When a nation falls to chaos then loyalty and patriotism are born.
> > ------------------------------ / Lao Tse /
> >
> >
> >
>
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: poll: cutoff for "high resolution"
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-05-15

Next message:
Subject: Re: UV light source for protein xtal detection
From: "V {- dot -} Nagarajan" tatoosh {- at -} GMAIL {- dot -} COM
Date: 2008-05-15