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.
- 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.
- 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
output.write_def_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
'pdb_1agy_res_SER_resID_129_del.pdb'.
- 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?
Thanks,
Alex