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
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