[phenixbb] confusing instruction for autoMR

[Randy Read]

Hi Maia,

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  
"copies_to_find=1 component_copies=2".

Regards,

Randy

On 12 Sep 2009, at 01:56, Maia Cherney wrote:

> Hi Tom,
> 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?
>
> Maia
>
> 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
>>
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>>
>>
>>
>
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------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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