[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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