In article <4mv8tu$far at mserv1.dl.ac.uk>, "M. Hough" <mhh> wrote:
?> Does anybody know how to calculate NCS operators for the following two cases.
?>
?> (1) Between two identical molecules in the asymmetric unit (Space group
41212)
?> ,
?> given the positions and MR - solutions for each.
?>
?> (2) Between the alpha1,alpha2 and beta1, beta2 subunits of hemoglobin.
?>
?> I need the above to use NCS averaging on my density maps
both cases are equivalent; just generate the two MR solutions and use
any superpositioning program to calculate the operator
in case you use O and RAVE, use the Lsq_explicit command in O or the
EXplicit command in LSQMAN
make sure to get the operator FROM the molecule around which the mask
will be generated TO the other molecule
e.g., in case (1) if solution #1 is in m1a.pdb and the other in m1b.pdb
and the mask will be around the first then do:
LSQMAN> read m1 m1a.pdb
LSQMAN> read m2 m1b.pdb
LSQMAN> expl m2 a1-999 m1 a1
LSQMAN> save m2 m1 rt_a_to_b.o .lsq_rt_m1a_tob
LSQMAN> save m2 m2 rt_unit.o .lsq_rt_unit
the file "rt_a_to_b.o" will contain the operator in O format, which
is recognised by O, RAVE, DM etc.; the file "rt_unit" will contain
the unit RT operator (i.e., from molecule 1 to molecule 1 itself)
--gerard
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Gerard J. Kleywegt
Department of Molecular Biology, Biomedical Centre
Uppsala University, Uppsala, SWEDEN
