Re: [ccp4bb] refmac

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

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

Previous message:
Subject: refmac
From: Alexandra Deaconescu deacona {- at -} BRANDEIS {- dot -} EDU
Date: 2009-11-18

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Subject: ... docking question
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-11-19

Subject: Re: refmac
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-11-19

Hi Alexandra,

the answers are in these papers and references mentioned in these papers
(list below is of course incomplete, but following the references inside
of these papers will give you the full picture):

# Jiang, J.-S. & Brunger, A. T. (1994). J. Mol. Biol. 243, 100-115.
"Protein hydration observed by X-ray diffraction. Solvation properties
of penicillopepsin and neuraminidase crystal structures."

# A. Fokine & A. Urzhumtsev. Acta Cryst. (2002). D58, 1387-1392. "Flat
bulk-solvent model: obtaining optimal parameters"

# P.V. Afonine, R.W. Grosse-Kunstleve & P.D. Adams. Acta Cryst. (2005).
D61, 850-855. "A robust bulk-solvent correction and anisotropic scaling
procedure"

Most recent CNS (1.2, I guess) has conceptually similar implemented as
described in "2005" paper above (as well as phenix.refine):

A.T. Brunger, Version 1.2 of the Crystallography and NMR System. Nature
Protocols 2, 2728-2733 (2007).

Pavel.

PS> Sorry, I'm not a right person to answer about what's behind specific
options in Refmac -:)

On 11/18/09 7:55 PM, Alexandra Deaconescu wrote:
> Hi everyone:
>
> Can someone enlighten me as to the difference between "simple" scaling
> and "Babinet scaling" in Refmac? It seems to me that Babinet scaling
> is more similar to what is employed in CNS for bulk solvent correction
> (Ksolv, Bsolv search). Is that correct? Would you recommend the
> Babinet method for high solvent content/ low resolution structures?
>
> Thanks a lot,
> Alex

CCP4bb navigation

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

Previous message:
Subject: refmac
From: Alexandra Deaconescu deacona {- at -} BRANDEIS {- dot -} EDU
Date: 2009-11-18

Next message:
Subject: ... docking question
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-11-19