[phenixbb] Fwd: Generate difference electron density maps for residues with multiple conformations

Alejandro Virrueta alejandro.virrueta at yale.edu
Wed Feb 17 11:51:51 PST 2016

Hello all,

I am trying to get the 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 whose occupancy I set to 0.
However, when I run the phenix.refine command (doing all of this via cli,
not gui), the output pdb file

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
   129 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.refine *pdb_del_file* *mtz_file* main.number_of_macro_cycles=5
output.write_eff_file=False output.write_geo_file=False
refinement.input.xray_data.r_free_flags.generate=True --overwrite

   - with *mtz_file *set to '1agy.mtz' (from the PDB) and *pdb_del_file* set
   to either 'pdb_1agy_res_SER_resID_120_del.pdb' and

   - This results in 2 files pdb_1agy_res_SER_resID_XXX_del_refine_001.mtz
   and 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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