[phenixbb] phenix.phaser multiple pdbs

G Y gysubscribe at gmail.com
Mon Aug 8 03:07:07 PDT 2011

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:


   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

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

Many thanks!

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