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

Alejandro Virrueta alejandro.virrueta at yale.edu
Thu Feb 18 09:39:06 PST 2016

I just tried phenix.maps, and it yields substantially different difference
maps than those obtained through my refinement process. Are there any other
techniques or parameters I can modify to make residues with multiple
conformations 'invisible' to phenix.refine, in addition/besides set
occupancies to 0 or deleting the residue form the pdb file?

On Wed, Feb 17, 2016 at 3:48 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Alex,
> 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.
> http://phenix-online.org/documentation/reference/phenix_maps.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_documentation_reference_phenix-5Fmaps.html&d=AwMDaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=erGJlXdJeX4XOslWBGLhRT0lLKKneOe9LsS9KwzY1H0&m=yk8Yay71IL1yLpt6JP2X6qX4HpzgJjlL51q_evgsG00&s=ZgesLYvmd_lhLM6nE_t0g1iPI2GN-1LFE-2NgeXd4oQ&e=>
> Pavel
> 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 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.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
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