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