[phenixbb] confusing instruction for autoMR
rjr27 at cam.ac.uk
Mon Sep 14 02:00:30 PDT 2009
The "copies" keyword is a shorthand for convenience in the common case
that both your model and the sequence refer to a monomer, and what it
does is set two separate keywords, copies_to_find and
component_copies, to the same value. If you want to set these
separately (e.g. you're searching for one copy of a dimer but your
sequence is for the monomer), then you should be able to say
On 12 Sep 2009, at 01:56, Maia Cherney wrote:
> Hi Tom,
> thank you for your reply. Still, the first question remains, if a
> has two identical copies, but the sequence is for a monomer, what
> 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,
>>>> 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
> phenixbb mailing list
> phenixbb at phenix-online.org
Randy J. Read
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