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

Pavel Afonine pafonine at lbl.gov
Wed Feb 17 12:48:07 PST 2016

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 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*Â 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*Â 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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160217/63c82323/attachment-0001.htm>

More information about the phenixbb mailing list