[phenixbb] phenix_automr error and autobuild question
Maike Bublitz
mbu at mb.au.dk
Fri Mar 23 06:35:05 PDT 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 <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:
>
> 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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