Re: [ccp4bb] Refining against images instead of only reflections

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: What is an aceptable spread in ADP values?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2010-01-28

Next message:
Subject: Re: Refining against images instead of only reflections
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-01-28

Subject: Re: Refining against images instead of only reflections
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2010-01-28

John Badger wrote:
>
>
> Diffuse scatter patterns were compared to simulations of correlated motions
> that were long-range (say, the size of the whole molecule) ...
>
>
This is exactly not the point I was trying to make. Anything confined
to a single unit cell is not what I would call "long range". As far as
I can tell, the only way for motions to introduce "extra" Bragg
intensity is for them to be "synchronized" across many unit cells. If
all cells are completely unsynchronized, then the occupancy-weighted
average electron density map of all the conformers will fully explain
the background-subtracted spot intensities, but if there is cell-to-cell
synchronization: it won't! The magnitude of the "unexplainable"
intensity change should be roughly proportional to the fraction of the
atoms that are "synchronously disordered", whether it be a TLS domain, a
two-headed side chain or what have you. It is not about whether all the
atoms in a TLS domain move together (they do), it is about whether a
given TLS domain in one cell is "in sync" with the same TLS domain in
the unit cell next door.

That's at least what I was trying to point out. I could be wrong.

I think what I am calling "synchronization" is called "order-disorder"
in some texts. I will need to read up on this and all the other
excellent reviews being posted in this thread. But, I don't think
phenomena like this has been investigated thoroughly for proteins
because only recently has enough computing power to do that become
available.
>
>
> From this perspective it is quite surprising that crystallographers are so keen
> on using TLS models for fitting displacement amplitudes.
Crystallographers have a very good reason for using TLS models: it makes
their R factors lower. ;)

-James Holton
MAD Scientist

CCP4bb navigation

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

Previous message:
Subject: Re: What is an aceptable spread in ADP values?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2010-01-28

Next message:
Subject: Re: Refining against images instead of only reflections
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-01-28