[phenixbb] confusing instruction for autoMR

[Maia Cherney]

Thank you, Randy.

Now it's clear.

Maia

Randy Read wrote:
> 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
> Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
> Hills Road                                    E-mail: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.                       www- 
> structmed.cimr.cam.ac.uk
>
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