[ccp4bb] build/refine individual methyl/metylene groups in membrane protein structures

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

Previous message:
Subject: Re: Refmac unrestrained refinement on ligands only
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-07-04

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Subject: Definition of Fourier coefficients
From: "Mayer, Mark (NIH/NICHD) [E]" mayerm {- at -} MAIL {- dot -} NIH {- dot -} GOV
Date: 2008-07-05

Subject: build/refine individual methyl/metylene groups in membrane protein structures
From: "Van Den Berg, Bert" Lambertus {- dot -} VandenBerg {- at -} UMASSMED {- dot -} EDU
Date: 2008-07-05

Hi all,

a common issue with membrane protein strustures is that at the end of refinemnt, there are (almost) always blobs of unassigned density covering the hydrophobic region that can't be built (because they are too small for a complete detergent molecule for example). Would it be feasible/allowed to build individual methyl/methylene groups in those blobs, much like is done for waters? Within CNS, what topology/parameter files would have to be used?

I seem to recollect a fairly recent membrane protein structure paper that introduced something like this, but for the life of me I can't remember the reference.

Cheers, Bert

Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: bert.vandenberg@umassmed.edu
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm

CCP4bb navigation

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

Previous message:
Subject: Re: Refmac unrestrained refinement on ligands only
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-07-04

Next message:
Subject: Definition of Fourier coefficients
From: "Mayer, Mark (NIH/NICHD) [E]" mayerm {- at -} MAIL {- dot -} NIH {- dot -} GOV
Date: 2008-07-05