Re: [phenixbb] MR error when fix one component and search for the other one

13 Jun 2012

      Hi,

Is it possible you're using an older version of Phenix?  There might have been a bug at some point if there was a mismatch between Phaser and the AutoMR Python script, but it seems to be fine now.  I've run a job testing the same functionality, using data available in $PHENIX/phenix_examples/beta-blip, in the current 1.8-1058 release.  This job finishes successfully:

--------- Content of automr.eff ------------
automr {
  build = False
  data = beta_blip_P3221.mtz
  crystal_info.space_group = P3221
  ensemble {
    ensembleID = "beta"
    copies_to_find = 0
    coords = beta.pdb
    identity = 100
    RMS = None
  }
  ensemble {
    ensembleID = "blip"
    copies_to_find = 1
    coords = blip.pdb
    identity = 100
    RMS = None
  }
  component {
    seq_file = "beta.seq"
    component_type = *protein nucleic_acid
    mass = None
    component_copies = 1
  }
  component {
    seq_file = "blip.seq"
    component_type = *protein nucleic_acid
    mass = None
    component_copies = 1
  }
  fixed_ensembles {
    fixed_ensembleID_list="beta"
    fixed_euler_list = 200.85 41.28 183.89
    fixed_frac_list = -0.496 -0.158 -0.281
  }
}
------- End automr.eff -----------

Job run with the following command: phenix.automr automr.eff

Best wishes,

Randy Read

On 12 Jun 2012, at 23:41, [email protected] wrote:
...
Hi everyone,
I am trying to fix one component from the previous MR search and try to search for the other one, euler and frac are taken from the pdb file of the previous run (MR.1.pdb). Here are my input file and error message.
Thanks in advance!
Fengyun
automr {
 build=false
 ensemble {
   ensembleID = "mol1"
   copies_to_find = 1
   coords = in.pdb
   RMS = 0.85
 }
 ensemble {
   ensembleID = "mol2"
   copies_to_find = 0
   coords = in.pdb
   RMS = 0.85
 }
 component {
   seq_file="mut.seq"
   component_type = *protein nucleic_acid
   component_copies = 4
 }
fixed_ensembles {
  fixed_ensembleID_list="mol2"
  fixed_euler_list = 206.66 146.75  96.21
  fixed_frac_list = 0.688 1.011 0.005
}
}
i get the error message like this,
ENSEMBLE: mol1 , 1 PDB file(s)
ENSEMBLE: mol2 , 1 PDB file(s)
Resolution set to  3.5
Specifying composition through protein sequence file /shared.scratch/ni/mut-p222-all/bb-3.5/AutoMR_run_5_/r2/mut.seq 4
Adding Ensemble  mol2  as fixed solution with:
Euler angles:  [206.66, 146.75, 96.21]
Coords (orthogonal A):  [0.688, 1.011, 0.005]
*************ERROR ENDING *******************
****************************************
AutoMR Input failed
Python argument types in
   SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float, bool, bool, bool)
did not match C++ signature:
   addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string, scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool, bool, scitbx::vec3<double>, double)
****************************************
*************ERROR ENDING *******************
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------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
Hills Road                                    E-mail: [email protected]
Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk