[phenixbb] Fwd: Generate difference electron density maps for residues with multiple conformations
pafonine at lbl.gov
Wed Feb 17 12:48:07 PST 2016
why use a cannon to kill a fly? phenix.refine is for refinement not map
calculation. I suggest to use more specific tools. phenix.maps should do
it, for example.
> I am trying to get theÂ difference electron density maps for residues
> with multiple conformations after I set the occupancy of their atoms
> to 0.
> My main goal is to visualize the green positive density peaks that
> should appear for the atoms whoseÂ occupancyÂ I set to 0.
> However, when I run the phenix.refine command (doing all of this via
> cli, not gui), the output pdb fileÂ
> I will try to illustrate my process and problem with an example that
> works fine and one that doesn't, side by side, step by step.
> 1. I generate a pdb file that has a chosen residue set to occupancy
> 0. See 'pdb_1agy_res_SER_resID_120_del.pdb' and
> 'pdb_1agy_res_SER_resID_129_del.pdb'. As you can see, the former
> has SER 120 set to 0 occupancy and has one conformation, and the
> latter has SER 129Â set to 0 occupancy for BOTH of its
> conformations. Both files are correct up to this point.
> 2. I then execute the following command:
> phenix.refineÂ *pdb_del_file*Â
> *mtz_file*Â main.number_of_macro_cycles=5 output.write_eff_file=False
> output.write_geo_file=False output.write_def_file=False
> refinement.input.xray_data.r_free_flags.generate=True --overwrite
> * withÂ *mtz_file *set to '1agy.mtz' (from the PDB) and
> *pdb_del_file*Â set to
> eitherÂ 'pdb_1agy_res_SER_resID_120_del.pdb' and
> * This results in 2
> filesÂ pdb_1agy_res_SER_resID_XXX_del_refine_001.mtz
> andÂ pdb_1agy_res_SER_resID_XXX_del_refine_001.pdb. Comparing
> these pdb files, you can see that the occupancy for SER 120
> remains set to 0 (which is what I want), but the occupancies for
> the 2 conformers for SER 129 have been filled in by phenix (not
> what I want) somewhere during the refinement process. As a result,
> I get the desired difference peaks for SER 120, but not for SER
> 129 (which seems to be averaged out).
> Other than deleting the 2nd conformation for SER 129, is there a way
> to solve this problem, preferably via command line arguments/flags?
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