Re: [ccp4bb] Refining alternate ligand/autoinhibition

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

Previous message:
Subject: difficulties to determine the space group
From: Schneider Sabine paxss2 {- at -} NOTTINGHAM {- dot -} AC {- dot -} UK
Date: 2007-05-08

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Subject: Re: difficulties to determine the space group
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-08

Subject: Re: Refining alternate ligand/autoinhibition
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-08

Well - A and B are meant to be flags to show there are 2 conformations
of a particular unit. sp they arent appropriate here and may be muddling
things up.

On the other hand you shouldnt get any repulsion between pairs of atoms
whose added occupancy is <= to 1.0

Is that always the case for your 2 scenarios?

Try removing the A and B flags and see if that is better.
Eleanor

Stefan Arold wrote:
> Dear All,
>
> I am having trouble refining a difficult case of alternate structures
> in REFMAC. In the crystal, two states superimpose:
> 1) Apo-protein with its own auto-inhibitory tail fixed into the ligand
> binding site
> and
> 2) Peptide-bound protein, where the peptide has displaced the
> auto-inhibitory tail.
> this also includes alternate side-chains of the protein ligand binding
> site, according to the apo state or peptide-bound state
>
> I was hoping that assigning 'A' and 'B' alternate states (for 'apo'
> and 'peptide-bound') to the protein chain (chain A)
> [ex:
> ATOM 62 C ATYR A 17 20.856 42.150 21.476 0.60
> 75.23 C]
>
> and state 'B' to the peptide
> [ex:
> ATOM 87 N BALA D 513 9.910 69.145 50.780 0.40
> 20.00 N]
>
> would do the job - but unfortunately, even though refmac refines this
> structure, the two states 'sense' each other, and refmac refinement
> applies repulsive forces, pulling the apo-auto-inhibitory tail and the
> peptide away from each other...
>
> Neither the refmac manual, nor the ccp4bb archives helped, so I
> thought one of you might...
>
> many thanks
>
> Stefan
>
>
>

CCP4bb navigation

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

Previous message:
Subject: difficulties to determine the space group
From: Schneider Sabine paxss2 {- at -} NOTTINGHAM {- dot -} AC {- dot -} UK
Date: 2007-05-08

Next message:
Subject: Re: difficulties to determine the space group
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-05-08