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 *******************

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

------ 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