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Re: [ccp4bb]: crystal and AU packing analysis

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The CCP4 program AREAIMOL can be used to analyse molecular solvent
accessible surface areas (asa) in a variety of situations - for example,
area buried in crystal packing can be examined using the DIFFMODE IMOL
option, see the documentation and the distributed example. It is also
straightforward for AREAIMOL to calculate the total asa for a single

If you are interested in area by subunit interactions then DIFFMODE
COMPARE is probably the one to use, though in this case you will
probably have to do some work in preparing input files (again, see
documentation and distributed example). (In all cases be careful to
choose the correct MODE, which tells the program how to treat solvent -
try to avoid using MODE ALL, since I think this can give unreliable

The CCP4 programs RWCONTENTS and MATTHEWS_COEF can be used to estimate
% solvent content.

For your supplementary question: Guoguang Lu's program WATNCS will pick
waters which follow NCS, and sort them out to the NCS asymmetric unit.

Hope this is useful, best wishes

Peter Briggs.

On Tue, 12 Dec 2000, Stefan Backstrom wrote:

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> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> Hello.
> I wonder what alternatives there are when one wants to analyze crystal
> packing surfaces (and surfaces within the AU).
> I would like to know the total area of a molecule, the area involved in
> packing to other molecules (in the AU and with symmetry related ones),
> solvent content et c.
> In CNS I could do this but it was very time consuming because I had to
> generate a pdb containing my AU and all symmetry related neighbouring
> molecules and analyze the possible packings one by one.
> Do you have any suggestions ?
> Oh, since I'm already bothering you, what program should I use to
> analyze NCS related waters ?
> Best wishes,
> Stefan
> -- 
> Stefan Backstrom
> Umea University
> s-901 87 Umea
> Sweden
> email: stefan.backstrom@ucmp.umu.se
> tel:	+46 907856794
> fax:	+46 90778007

Peter J Briggs, pjx@dl.ac.uk   Tel: +44 1925 603455
CCP4,         ccp4@ccp4.ac.uk  Fax: +44 1925 603124
Daresbury Laboratory, Daresbury, Warrington WA4 4AD