[phenixbb] MR error when fix one component and search for the other one
Randy Read
rjr27 at cam.ac.uk
Wed Jun 13 01:14:42 PDT 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, fn1 at rice.edu 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
> phenixbb at phenix-online.org
> 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: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
More information about the phenixbb
mailing list