The molecular replacement program does not know about your molecule
being a single polypeptide chain. The problem is "fit two bodies"
therefore the program fits two bodies. The centre of mass of whatever
you wish to position is placed the "standard asymmetric unit" used by
the program. If it happens that the center of mass of the second domain
- linked to the (already positioned) first domain by the polypeptide
linkages - does not fall within that asymmetric unit, then it won't be
this one that will be provided in the resulting pdb file. An equivalent
will be provided. Checking the symmetry equivalents (including limited
translations) and writing out the "correct" equivalent to replace that
you do not wish to have is the way to go. Just as you did. In case of a
search using the entire molecule, this "problem" does not occur.
And if you go from a molecular replacement solution provided by program
X to an automatic model rebuilding program called Y, these two programs
will not necessarily use the same conventions. Hence you may end up with
the model after automatic model rebuilding that does not superimpose
with the input file coming from molecular replacement. Same reason there.
Does that answer your question?
Fred.
Christian Roth wrote:
Dear all,
I tried MolRep with a two domain protein. I have cut the two domain as one
domain rotates which prevent a search with the complete model. After I finished
the first run. I put this solution as fixed input model in the second molrep run
with the second domain. The resulting solution positioned the tow expected
molecules, but not nearby the two already found domains. Interestingly a
symmetry mate would be at the correct position. I could manually write out the
coordinates of the symmetry molecule to put the two domains together, but I
thought Molrep would position it close to the already found domains because
they belong together and in fact they are one polypeptide chain.
Why does this not happen? Do I have to incorporate additional information or
constrains for the Molrep run?
Thanks and Best Regards
Christian
