Overview

A polder map is an omit map which excludes the bulk solvent around the omitted region. This way, weak densities, which can be obscured by bulk solvent, may become visible. Typical omitted regions are:

• ligands
• residues protruding into solvent area and with unclear side chain orientations (such as lysine, arginine, etc.)
• C- or N-terminal residues

It is not recommended to omit large portions of the model at once (as the excluded bulk solvent volume might become too large) or to omit single atoms. Instead: several residues or one ligand are typical selections for polder maps. It should be kept in mind that phenix.polder does map calculations, no bias-removal strategies (such as refinement, annealing, etc.) are applied.

A presentation file with examples can be found here.

Running the program

phenix.polder is executed via the command line:

% phenix.polder model.pdb data.mtz selection='chain B and resseq 3'

This command calculates an omit map of residue 3 in chain B. Common file formats are supported (.pdb and .cif for models; .mtz, .hkl files for data). The syntax for the selections is the same as used by other phenix tools.

Output of phenix.polder consists of a single MTZ file, named polder_map_coeffs.mtz by default. This file will contain amplitudes and phases for two maps:

• mFo-DFc_polder: map coefficients of polder omit map
• mFo-DFc_omit: map coefficients for omit map where bulk solvent floods into omitted region. It is equivalent to remove the selection from the model and to calculate a difference map. This map can be used for comparison with the polder map.

Both map types require you to load them manually in Coot, by choosing the "Open MTZ, mmCIF, fcf or phs..." option and by activating the "Is a Difference Map" option in the window which opens after choosing the filename.

Other options

There are several other programs in Phenix for calculating omit maps.

• phenix.composite_omit_map can produce relatively bias-free maps by computing a number of omit maps covering specific regions, and then combining the areas around the omitted regions. Default options allows the bulk solvent mask to extend into the omitted region
• phenix.refine can be used to manually generate omit maps for a smaller selection of the model by specifying the omit_selection keyword. The single-omit mode of the composite omit map program is equivalent to this.
• phenix.maps can generate simple omit maps without refinement.

Reference

in preparation

List of all available keywords

• job_title = None Job title in PHENIX GUI, not used on command line
• model_file_name = None Model file name
• solvent_exclusion_mask_selection = None Atoms around which bulk solvent mask is set to zero
• reflection_file_name = None File with experimental data (most of formats: CNS, SHELX, MTZ, etc).
• data_labels = None Labels for experimental data.
• r_free_flags_labels = None Labels for free reflections.
• sphere_radius = 5 Radius of sphere around atoms where solvent mask is reset to zero
• high_resolution = None High resolution limit
• low_resolution = None Low resolution limit
• scattering_table = *n_gaussian wk1995 it1992 neutron electron Scattering table for structure factors calculations
• resolution_factor = 0.25 Used to determine the grid step = resolution_factor * high resolution
• output_file_name_prefix = None Prefix for output filename
• mask_output = False Additional output: ccp4 maps containing the solvent mask for inital model (mask_all.ccp4), when ligand is omitted (mask_omit.ccp4) and the mask used for polder (mask_polder.ccp4).
• debug = False Additional output: biased omit map (ligand used for mask calculation but omitted from model)
• guiGUI-specific parameter required for output directory
  • output_dir = None