From: [email protected] [[email protected]] on behalf of Maike Bublitz [[email protected]]
Sent: Friday, March 23, 2012 7:35 AM
To: [email protected]
Subject: Re: [phenixbb] phenix_automr error and autobuild question

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 <[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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