Re: Amore solutions -> CCP4 asymmetric unit

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Martin Laurberg wrote:
> 
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> 
> - Is there a program to transfer Amore solutions into the CCP4 asymmetric
> unit ? ( - just redefining rotation and translation from the Amore output)
> 
> Martin
> 
> --
> Martin Laurberg
> Molecular Biophysics
> Lund University
> Sweden


 Any MR program is simply going to find a CRYSTALLOGRAPHIC solution, and
not care about building a sensible model..
 My approach is a) always shift the first molecule to have translations
betwen -1/2 and 1/2.

( I assume you apply the solution to the coordinate file OUTPUT from the
TABFUN run, which has its centre of mass at (0,0,0)
 by this procedure:
pdbset xyzin tabfun_out.pdb xyzout soln1.pdb
cell a B C alpha beta gamma ( new cell)
rota euler ALPHA BETA GAMMA
shift frac Tx Ty Tz
CHAIN A
end

Then for further molecules you may well want a symmetry equivalent of
the Amore solution to build up a tetramer or something.

 Easiest way - generate  all molecules from the Amore solutions with
different cHAIN IDs and make one coordinate file.
Then run distang xyzin all_solns.pdb 
SYMM whatever
RADI CA 4
dist VDW

END

 That will give you contacts between molecules with symmetry codes: eg 2
-1 0 1

 There are various choices, but once you see that maybe there are better
contacts between molecule 1 and molecule 2 using Symmetry  2 -1 0 1
you would generate a new version of molecule 2; eg 
pdbset xyzin soln2.pdb xyzoutout soln2a.pdb 
SYMGEN -X-1, Y+1/2,-z+1 for symmetry    2 -1 0 1 in spacegroup P21


 Then rebuild the solnsall.pdb with the new soln2a.pdb and run distang
again.

You are aiming to get a nice compact molecule with good contacts
produced by symmetry X,Y,Z

generated by particular symmetry operators.


 Can be messy but it saves a lot of timew on the graphics later!
Eleanor