I like Eleanor’s suggestion of using PISA to find the assemblies automatically. That’s probably the best thing to do first.
However, there’s an alternative I like that uses your brain’s pattern-matching abilities. In coot, view your molecules as C-alpha traces and display a generous number symmetry copies, also as C-alpha. Center on an atom in one of the monomers (either use Draw->Go to atom, or middle click followed by the “p” key so that coot really knows you’re centered on that atom). Then just repeatedly hit the “o” key, which goes to the same view of the next NCS-related monomer. As you’re running through them, keep an eye on the neighbours, to see if any relationship among neighbours always recurs. This can also be a useful way to get a hint of missed symmetry, because then there will be views that should have a different packing environment but nonetheless look the same!
Best wishes,
Randy Read
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
> On 7 Jun 2016, at 17:22, Sudhaker D <[log in to unmask]> wrote:
>
> Dear sir/madam,
> Recently i have submitted a PDB at RCSB (PDB deposit). the protein is crystallised in C121phase group and there are six asymmetric molecules are present in Unit cell, I have got few comments from wwPDB annotation, one of which is given below in the name of Biological assembly
>
> Biological Assembly
> You reported that the biological assembly of this structure is dimeric.
> But we could not make the complete three dimer using all chains.
> We presumed that chain B and D make the dimer, chain e and F make the dimer.
> But chain A and C did not make the correct dimer.
> If the biological assembly should be dimeric,
> would you please provide the information of three dimers ?
> e.g. B+D = dimer1, E+F=dimer2, A+ moving C with symmetry operation -x,y,1-z= dimer3, et c.
>
>
> So please kindly give me suggestions, how to find out symmetry operations and -x,y,1-z for dimer three
>
> Regards
> sudhaker
> --
>
> Sudhaker Dharavath
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067.
> +919013926882.
>
> http://www.jnu.ac.in/Faculty/gourinath/Lab_Members.htm
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