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 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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So why are geometry restraints imposed on multiple conformers but not a single conformation, with both having atoms set to 0 occupancy? On Thu, Feb 18, 2016 at 2:09 PM, Pavel Afonine wrote:

Hi Alejandro,

I just tried phenix.maps, and it yields substantially different difference

...

maps than those obtained through my refinement process.

not surprising at all because phenix.refine changes the model and phenix.maps uses input model as is to compute maps!

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?

No. They will be always visible to geometry restraints.

Pavel