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: [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
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 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb