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
