[phenixbb] Fwd: Generate difference electron density maps for residues with multiple conformations
alejandro.virrueta at yale.edu
Wed Feb 17 11:51:51 PST 2016
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
- 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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