Partial molecular replacement

[Eleanor Dodson <ccp4@yorvic.york.ac.uk>]

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On Jul 29,  5:28pm, Jinsong Liu wrote:
> Subject: partial molecular replacement
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>
.......
> I have been always wondering if it can be soleved by molecular replacement in
> the recipical space, not in the real space like ESSENS. Which program can
deal
> with it? I have a MAD phase, and 80% model fixed, how to use the NMR model to
> solve the rest of the structure? CAn Amore handle this?
>


 We have sometimes got MR solutions to problems like this, but it may not be
the easist way!

 The traditional way is to fix your 80% model;
 ( put them into TABFUM with the NOROTAT option; then the SOLUTIONRC will have
angles 0 0 0, and you can either run the TRAFUN stage, or just remember that
the solution will be the reverse of the centre-of-mass shift in TABFUN)

 Then make a second model from the NMR structure, run SOLUTIONRC with that
against all the data, where you would expect a very very weak signal..)

 then run TRAFUN again TABLE1 80%.tab TABLE2 nmr.tab
  with NMOL 2
 SOLUTIONTF1 FIX 1 80% one
  and all the s from the NMR model ( remember to put
SOLUTIONRC  2   ( to refer to TABLE2 )

 then you might pick out the answer..



A more sophisticated one is to mask out all the density from the 80% model from
your SHARP map

 ( overlapmap will do this.. use sfall to make an ATMMAP from the 80%, then
overlapmap with the keyword EXCLUDE to set all the grid points where there is
80% density to 0.00)

 Then you can use sfall again to generate structure factors from the remaining
grid points; which should correspond to the remaining 20% model, and run Amore
between those SFS as the hklin, and the NMR model..
 If you could get a ROTFUN solution you could also use the phases again to run
a phased translation.


 May work!  Let me know if it does!

 Eleanor Dodson

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Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65
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