[phenixbb] phenix.phaser multiple pdbs

Dr G. Bunkoczi gb360 at cam.ac.uk
Mon Aug 8 06:13:21 PDT 2011


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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