Re: [phenixbb] phenix_automr error and autobuild question

23 Mar 2012

      Thank you Nat,

Phaser-MR (from the GUI) worked fine with the fixed ensemble.

But for the autobuild problem - it does run if I provide an mtz file 
with phases derived from the known part of the model for the initial 
map, but it seems to ignore the pdb file which I define as ligand and 
obviously tries to build the whole thing - which fails.
Here are some of the parameters I have defined in the .eff file. Am I 
missing something?

autobuild {
   data = mydata_phased_with_partial_model_in_sigmaa.mtz
   model = None
   seq_file = component_to_build.fasta
   map_file = mydata_phased_with_partial_model_in_sigmaa.mtz
   refinement_file =mydata_phased_with_partial_model_in_sigmaa.mtz
   hires_file = Auto
   input_files {
     input_labels = FP SIGFP PHIC WCMB None None None None FreeRflag
     input_map_labels = FP PHIC WCMB
     input_refinement_labels =FP SIGFP FreeRflag
     input_lig_file_list = refined_known_component.pdb
     keep_input_ligands = True
     keep_input_waters = False
     keep_pdb_atoms = True
     refine_eff_file_list = None
     map_file_is_density_modified = False
     map_file_fom = None
     use_map_file_as_hklstart = False
     use_map_in_resolve_with_model = False
   }
   model_building {
     build_type = *RESOLVE RESOLVE_AND_BUCCANEER
     include_input_model = False
     refine = True
     two_fofc_in_rebuild = False
     refine_map_coeff_labels = "2FOFCWT PH2FOFCWT"
     filled_2fofc_maps = True
     map_phasing = False
   }
   rebuild_in_place {
     rebuild_in_place = Auto True *False
   }

Best regards,
Maike

On 22.03.2012 14:33, Nathaniel Echols wrote:
...
On Thu, Mar 22, 2012 at 6:23 AM, Maike Bublitz mailto:[email protected]> wrote:
1) I have trouble getting a molecular replacement job to run
    (Phenix Version 1.7.3-928), where I want to keep one ensemble
    fixed in its known orientation, only looking for a second
    ensemble. I keep on getting the following error message, both from
    the GUI and from command line (using a 'mymr.eff' parameter file):
****************************************
    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 *******************
I can't figure out what I'm doing wrong. Any suggestions?
This is definitely a bug.  Two suggestions: a) try the Phaser-MR GUI 
instead, it may not have this problem, or b) update to the latest 
nightly build and see if it's fixed there.  I will see if we can add a 
regression test for specifying a fixed ensemble.
...
2) Which parameters would I need to specify to let phenix.autobuild 
build a model for one protein of a 2-component complex from scratch, 
while keeping the other component unchanged (and using it to calculate 
the phases)? Is that possible?
I think you need to define the existing component as ligands, as 
described here:
https://www.phenix-online.org/version_docs/dev-1012/autobuild.htm#anch103
I suspect this means that you'll need to supply an initial map for 
phases, rather than having it calculate them from the "ligands", but 
I've never actually tried this myself.
-Nat
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