Dear all,

To those who are interested in the phenix.polder tool:

An "official" announcement and a detailed description on how to run phenix.polder will come soon. However, here is some more information for those who already want to try the tool.

Polder calculates omit maps by excluding the bulk solvent mask to flood into the area of the atom selection. So they might be effective for atom selections in binding pockets and around the surface of the protein. Atom selection can be f.ex. a ligand or a protein residue.

How to run: phenix.polder model.pdb data.mtz selection="chain A and resseq 123"

The selection should be one ligand or one residue. I do not recommend choosing a very large selection, such as several ligands or large number of residues at once.

To look at the map, open "polder_map_coeffs.mtz" (which has been created by polder) in COOT, using the "Open MTZ, mmCIF, fcf or phs" option, and by checking the box "Is a difference map". Then choose map coefficients "mFo-DFc_polder" and corresponding phases.

If you want to compare to an omit map which has been calculated by deleting the atom selection from the model, open "mFo-DFc_omit".

Let me know if you have questions.

Best wishes,

Dorothee

On Thu, Feb 25, 2016 at 9:09 AM, Pavel Afonine <pafonine@lbl.gov> wrote:

Hi Huanwang,

it needs to contain diffraction data, Fobs (Iobs) and (optionally) free-r flags.

Pavel

On 2/25/16 08:55, Huanwang Yang wrote:

Dear Pavel,

Thanks you so much for the new tool which will be useful to the density validation.

I have a question about the mtz file that is provided to the phenix.polder.
1. Does it have to contain the map coefficients such as FOFCWT/PHFOFCWT?
2. If the mtz must contains the FOFCWT/PHFOFCWT, do you have a simple tool that will calculate the map coefficients using your bulk solvent method?

Thanks a lot.

Huanwang

On 02/25/2016 11:29 AM, Pavel Afonine wrote:

Hi Alex,

This is not exactly phenix specific, but I was wondering what are some commonly used methods to determine and validate the presence/occurrence of multiple conformations for a given amino acid?

I just realized it myself yesterday that most efficient (in terms of finding answer) way is to use new Phenix tool called phenix.polder (a new tool being developed in our team in order to better visualize weak densities in residual Fo-Fc maps), which is available in latest nightly build. Example:

phenix.polder model.pdb data.mtz selection="chain A and resseq 123"

where "chain A and resseq 123" selects residue in question (this assumes you have placed one copy of residue conformer).

Pavel

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