Suggestions:
Are you using the GUI - that gives you a molrep option to provide a
fixed model..
Re Amore - yes you can do this - run first pass as autoamore which
should find one monomer,
the keep on redoing the TRAN fun providing the solution to 1st, 1st+2nd,
etc as "known solution" - all done in GUI..
Some hints - if you have 4 monomers is there a non-crystallographic
translation? MOLREP will report this..
If that NC translation has a coordinate as 0.5 then this will generate
misleading absences along that axis and the SG may actaully be P 2 21 21
or P21 2 21 or P 21 21 2 depending on the axis..
And if you expect a dimer why not use that as your search model?
Also try PHASER - it is often good but you may need to ask for less
stingent packing checks than the default
Eleanor
David Roberts wrote:
> Hi all,
>
> I'm relatively new to using CCP4 (I've done most of my crystallography
> using x-plor, phases, etc...). But, I like ccp4, and so I'm using it in
> concert with amore (which I know is part of the ccp4i build now) for
> molecular replacement.
>
> I have a protein that I'm working on with data collected from Argonne.
> There are many forms, and I have several of these forms collected (metal
> bound, apo, mutants, etc...). I have a solution for a wild-type form,
> and am presently working on solving a mutant form. For molecular
> replacement, I used the wild type structure (obviously). It's a
> homodimer, so I tried using both the monomer and the dimer form of the
> protein (it's possible that the mutant is conformationally different
> from the wild type, so it's not a clear-cut problem).
>
> Furthermore, they both crystallize in the same space group (P212121),
> but unit cells are different (I don't have the exact numbers now, but
> the general idea is the wild type is 30/60/120, while the mutant is
> 60/70/120). As a result, the wild type has 2 monomers per asu while the
> mutant has 4 (I think).
>
> When I look at results from mol rep (ccp4i, auto-molrep routine), I get
> 4 molecules per asu with the monomer as a search. 2 of the molecules I
> think are right (map is good - they form a good dimer, etc...), while I
> think 2 are incorrect (the dimer overlaps, and it just doesn't look good).
>
> My question - finally - how can I run automolrep with one dimer fixed,
> looking for the location of the other 2 monomers (so basically I want to
> fix a dimer as part of my solution, and then search for the other 2
> molecules in the asu). I know it's probably simple and possible, but
> it's not a world I am very familiar with (I seriously have just done MIR
> structures, they are easy for me, I have had very little work with mol
> rep). Could I do this with Amore as well (so fix 2 molecules and then
> look for an additional 2 using amore).
>
> Thanks for the help. Have a great week-end
>
> Dave
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