[phenixbb] phenix.phaser multiple pdbs

[G Y]

Dear Gabor,

Thanks a lot for your detailed explanation and kind help. I tried your
comment. The two ways of defining search procedure gave me the same
solution.

For

search {
 ensembles = a1
 copies = 1
}
search {
 ensembles = a2
 copies = 1
}

I got also only one result contains one best molecule pdb. Would you have
some idea for this? How could I really get several output for each of the
input model?

Thanks and regards,
G



On Mon, Aug 8, 2011 at 3:13 PM, Dr G. Bunkoczi <gb360 at cam.ac.uk> wrote:

> Dear G,
>
> after carefully re-reading your email, I think I have only given half of
> the answer. By repeating the 'coordinates' scope, you are defining one
> ensemble using multiple PDB files. If you want to define multiple ensembles,
> you need to repeat the whole ensemble scope, i.e.
>
>
> ensemble {
>  model_id = a1
>  coordinates {
>    pdb = model1.pdb
>    identity = 0.9
>  }
> }
> ensemble {
>  model_id = a2             <= note the change in model_id
>
>  coordinates {
>    pdb = model2.pdb
>    identity = 0.9
>  }
> }
>
> If you want Phaser to actually search for all these ensembles, you need to
> add a search keyword as well:
>
> 1. Conduct a separate search for each ensemble listed. The search order is
> decided automatically. The solution contains one molecule of a1 + one
> molecule of a2.
>
> search {
>  ensembles = a1
>  copies = 1
> }
> search {
>  ensembles = a2
>  copies = 1
> }
>
>
> 2. Phaser will search for each alternative ensembles in turn and pick the
> best one (the solution will contain one molecule of a1 or one molecule of
> a2, but not both):
>
> search {
>  ensembles = a1,a2
>  copies = 1
> }
>
> HTH, Gabor
>
>
>
> On Aug 8 2011, Dr G. Bunkoczi wrote:
>
>  Dear G,
>>
>> I think 'coordinates' is a multiple scope, so you have to define your
>> ensemble as follows:
>>
>> ensemble {
>>  model_id = a1
>>  coordinates {
>>    pdb = model1.pdb
>>    identity = 0.9
>>  }
>>  coordinates {
>>    pdb = model2.pdb
>>    identity = 0.9
>>  }
>>  coordinates {
>>    pdb = model3.pdb
>>    identity = 0.9
>>  }
>>  coordinates {
>>    pdb = model4.pdb
>>    identity = 0.9
>>  }
>> }
>>
>> BW, Gabor
>>
>> On Aug 8 2011, G Y wrote:
>>
>>  Dear all,
>>>
>>> I am writing a bash script for running phenix.phaser automatically on an
>>> ensemble of multiple pdbs. These pdbs have been superimposed by other tools
>>> before running phaser.
>>>
>>> The following is what I wrote for the ensemble part in params.eff file:
>>>
>>> ensemble {
>>>  model_id = a1
>>>  coordinates {
>>>    pdb = model1.pdb
>>>    pdb = model2.pdb
>>>    pdb = model3.pdb
>>>    pdb = model4.pdb
>>>    rmsd = None
>>>    identity = 0.9
>>>  }
>>>
>>> It runs well. When it finished, I want to confirm that it really run MR
>>> on
>>> all four models or on a ensemble of these models. However in .log file, I
>>> found at the refinement part it shown me:
>>>
>>> ----------
>>> REFINEMENT
>>> ----------
>>>
>>>  There is 1 solution to refine
>>>  Refining solutions
>>>  0% 100%
>>>  |==| DONE
>>>
>>>
>>>  Configuring ensembles
>>>  ---------------------
>>>  PDB file # 1: model1.pdb
>>>     This pdb file contains 1 models
>>>     The (input) RmsD of this model with respect to the real structure is
>>> 0.8
>>>
>>> **************************** Does this mean that phenix.phaser only run
>>> MR with the first model? Does it due to the way I wrote in my params.eff
>>> file? What would be the correct way?
>>>
>>> Many thanks!
>>>
>>> best,
>>> G
>>>
>>>
>>
>>
> --
> ##############################**####################
>
>    Dr Gabor Bunkoczi
>
>    Cambridge Institute for Medical Research
>    Wellcome Trust/MRC Building
>    Addenbrooke's Hospital
>    Hills Road
>    Cambridge CB2 0XY
> ##############################**####################
>
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