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Re: Amore solutions -> CCP4 asymmetric unit
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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 Laurberg
> Molecular Biophysics
> Lund University
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
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
RADI CA 4
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
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!