Re: [ccp4bb] refinement of half molecules

- Protein crystallography

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

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Subject: Re: Reading the old literature / truncate / refinement programs
From: "Ian J {- dot -} Tickle" i {- dot -} tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-10-03

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Subject: Summary: log tools for crystallization conditions
From: "S {- dot -} Thiyagarajan" tyahaa {- at -} YAHOO {- dot -} COM
Date: 2008-10-03

Subject: Re: refinement of half molecules
From: Lijun Liu liulj {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-10-03

For sure you could do it by these softwares with occ. set to 1/2 (and
in case some restrictions need to be released),
if what you mentioned were the TRUTH.

But before doing this, you may want to check the possibilities of 1)
misindexing and 2) twinning.
MR solution with 1/2 z translation fit as well does not have to mean a
new solution nor imply that crystal pathology!

> Hey all,
>
> I have a structure where two (identical) half molecules occupy one
> unit cell but are shifted by half a unit cell translation. I would
> like to refine them concurrently with global occupancy for each
> protein fixed to 1/2 initially (maybe relax that later). Is that
> possible in refmac and how? How about phenix, CNS?
>
> Thank you.
>
>
> Andreas
>
>
>
> Some more details for those interested in crystal pathologies. A
> fraction of the unit cells making up the crystal are shifted by half
> a unit cell translation in a statistic manner (peak in native
> Patterson at 0.5z). The structure was solved by MR with one
> molecule per au but doesn't refine. There is good density for the
> MR solution, but the solution shifted by 1/2 z fits the density
> nearly as well.
>
>
>
> --
> Andreas Förster, Research Associate
> Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London

Lijun Liu, PhD
Institute of Molecular Biology
HHMI & Department of Physics
University of Oregon
Eugene, OR 97403
541-346-5176

CCP4bb navigation

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

Next message:
Subject: Summary: log tools for crystallization conditions
From: "S {- dot -} Thiyagarajan" tyahaa {- at -} YAHOO {- dot -} COM
Date: 2008-10-03