Re: [ccp4bb] Zero occupancy and bad geometry

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

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Subject: Re: qualification to serve as the co-author for the protein 3D structure stored in RCSB
From: Eleanor Dodson eleanor {- dot -} dodson {- at -} YORK {- dot -} AC {- dot -} UK
Date: 2012-03-07

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Subject: How to reduce no. of overlaps
From: Dipankar Manna dipankar_m {- at -} AURIGENE {- dot -} COM
Date: 2012-03-07

Subject: Re: Zero occupancy and bad geometry
From: Eleanor Dodson eleanor {- dot -} dodson {- at -} YORK {- dot -} AC {- dot -} UK
Date: 2012-03-07

Coordinates with occ > 0 are refined and may shift - cds with occ=0 stay
where they were.. This may result in bad geometry of course. You can
"reglise" the whole residue in coot but that doesnt do nything except make
it look tidier.. Eleanor

On Mar 7 2012, Joel Tyndall wrote:

>Hi folks,
>
> I have a case where I have changed the occupancy of a lysine residue to
> 0.00 and after refinement the geometry is wrong, i.e. one of the bonds is
> extended (no connectivity in Coot and length is 1.76A). I have seen this
> before with other residues and a previous data set. The break in this
> case occurs between CG (1.00 occ) and CD (0.00 occ).
>
>Any thoughts on why this is occurring?
>
>Cheers
>
>Joel
>
>_________________________________
>Joel Tyndall, PhD
>
>Senior Lecturer in Medicinal Chemistry
>National School of Pharmacy
>University of Otago
>PO Box 56 Dunedin 9054
>New Zealand
>Skype: jtyndall
>http://www.researcherid.com/rid/C-2803-2008
>Pukeka Matua
>Te Kura Taiwhanga Putaiao
>Te Whare Wananga o Otago
>Pouaka Poutapeta 56 Otepoti 9054
>Aotearoa
>
>Ph / Waea +64 3 4797293
>Fax / Waeawhakaahua +64 3 4797034
>
>

--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266

CCP4bb navigation

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

Next message:
Subject: How to reduce no. of overlaps
From: Dipankar Manna dipankar_m {- at -} AURIGENE {- dot -} COM
Date: 2012-03-07