[phenixbb] confusing instruction for autoMR
chern at ualberta.ca
Fri Sep 11 17:56:09 PDT 2009
thank you for your reply. Still, the first question remains, if a model
has two identical copies, but the sequence is for a monomer, what number
of copies should I use: of model or of monomers?
Thomas C. Terwilliger wrote:
> Hi Maia,
>>> This is the example from the website:
>>> Run AutoMR using coords.pdb as search model, native.sca as data, assume
>>> RMS between coords.pdb and true model is about 0.85 A, the sequence of
>>> true model is seq.dat and there is 1 copy in the unit cell:
>>> phenix.automr coords.pdb native.sca RMS=0.85 seq.dat copies=1 \
>>> n_cycle_rebuild_max=2 n_cycle_build_max=2
>>> 1. 1 copy of what: model.pdb or seq.dat? Model.pdb could be a dimer and
>>> seq.dat a monomer.
> In this example we are assuming that model.pdb is a monomer and seq.dat is
> the sequence of that monomer.
>>> 2. 1 copy in the unit cell. Is it really in the unit cell? Usually we
>>> use number of copies in the asymmetric unit.
> That one is a very bad typo. Yes, I meant one in the asymmetric unit. I
> have just fixed that in the documentation...
> All the best,
> Tom T
> phenixbb mailing list
> phenixbb at phenix-online.org
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