[phenixbb] confusing instruction for autoMR

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Sep 11 16:45:06 PDT 2009

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

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