[phenixbb] phenix.phaser multiple pdbs

Dr G. Bunkoczi gb360 at cam.ac.uk
Mon Aug 8 04:25:52 PDT 2011


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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