[phenixbb] phenix_automr error and autobuild question

Terwilliger, Thomas C terwilliger at lanl.gov
Fri Mar 23 12:55:22 PDT 2012

Hi Maike,

What you are doing looks like it should work, however you might want to use this value for keep_pdb_atoms:

   keep_pdb_atoms=False  #keep the ligand atoms if model (pdb) and ligand overlap

because as it is you will take the atoms from the model that autobuild builds if
they overlap with the ones from your input model. Note that autobuild will
try to build everything...and then in places where your input model is present, it
should be used. If that isn't happening, please let me know and I'll try to
figure out why.
All the best,
Tom T
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Maike Bublitz [mbu at mb.au.dk]
Sent: Friday, March 23, 2012 7:35 AM
To: phenixbb at phenix-online.org
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 {
    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,

On 22.03.2012 14:33, Nathaniel Echols wrote:
On Thu, Mar 22, 2012 at 6:23 AM, Maike Bublitz <mbu at mb.au.dk<mailto:mbu at mb.au.dk>> 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:


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.


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