Re: [ccp4bb]: MR problems

["David J. Schuller" <djs63@cornell.edu>]

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On Thu, 22 Mar 2001, Neratur K Lokanath wrote:

> I am trying to solve the structure using MR method using
> CCP4.
> And can i split the pdb file into two pdb files, then could
> i fix the one on the another? or what are the possibilities
> to get the solution?

this is not clear.  are there 2 copies of the search model molecule in the
original PDB file? if so, do they form a biological dimer?
or are you talking about breaking a single molecule into 2 domains?

if your search model forms a dimer and you expect your target molecule to
have the same dimer interface, it is your choice whether to search with a
monomer or a dimer. (or try both and take the one that works)

if there are 2 or more identical molecules in the search model but their
relationship is crystallographic and not biological, you probably should
search with a monomer. you could also superimpose them and search with the
resulting suite of molecules.  this has been used successfully before.

if you have a single molecule in the search model and wish to search with
only part of it at a time, that should also be acceptable, providing you
don't choose too small of a portion. AMoRe is capable of handling multiple
non-identical search models. the strategy would be to locate one domain,
FIX it, then search for the other.

you may do whatever you wish with the search model.  i frequently convert
my search models to poly-alanine representations, with good success.  if
a part of the search model has no equivalent in the target, you may clip
it off.

if you need more help, please clarify your question.

=======================================================================
                       "Reality:  What a gyp."  - Dogbert
=======================================================================
                        David J. Schuller
                        modern man in a post-modern world
                        MacCHESS, Cornell University
                        djs63@cornell.edu