OccuPy 0.1.3

OccuPy: A local map scale estimation for cryo-EM maps

A fast and simple python module and program to estimate local scaling of cryo-EM maps, to approximate occupancy, and optionally also equalise the map according to occupancy while suppressing solvent amplification.

Estimation of occupancy

The primary purpose of OccuPy is to estimate the local map scale of cryo-EM maps. All regions in a cryo-EM map have pixel values that can be considered as drawn from some distribution. In well-resolved regions noise has been cancelled such that this distribution contains values above and below solvent. Decreased resolution or occupancy converesely results in values that are closer to solvent. OccuPy locates a region that exhibits the highest level above solvent, and utilizes this to place all other regions on a nominal scale between 0 and 1. This is a proxy for occupancy, under the assumption that there is limited flexibility. In maps exhibiting flexibility, the estimated map scale does not strictly represent occupancy, as OccuPy does not presently separate these factors in map value depreciation.

Amplification of partial occupancies

OccuPy can also amplify confidently estimated partial occupancy (local scale) in the input map by adding the --amplify option. By default this will set --amplify-amount 1, meaning that regions of confident intermediate scale (occupancy) are elevated up to the same nominal occupancy (100%). Values lower than 1 amplify intermediate occupancies, but incompletely. These regions can equally be attenuated, by specifying an --amplify-amount less than 0, down to -1. This acts as an exponent on the amplification, such that further decreasing it (below -1) will further attenuate low occupancies, but this is not recommended or tested. Values in the range [-1,1] are thus meaningful.

Solvent supression

Map scale amplification by inverse filtering would result in an extremely noisy output if solvent was permitted to be amplified. To mitigate this, OccuPy estimates a solvent model which limits the amplification of regions where the map scale is estimated as near-solvent. One can aid this estimation by providing a mask that covers non-solvent, permitting OccuPy to better identify solvent. This need not be prcise or accurate, and OccuPy will amplify map scale outside this region if it is confident about the scale in such a region . This is thus not a solvent mask in the traditional sense, but rather a solvent definition. Additionally, the estimation of the solvent model does NOT affect the estimated map scaling in any way, only the optional amplification.

The supression of solvent is not contigent on amplification - one can choose to supress solvent regions or not, irrespective of amplification. This acts as automatic solvent masking, to the extent that OccuPy can reliably detect it.

Expected input

OccuPy expects an input map that has not been solvent-flattened (there should be some solvent somewhere in the map, the more the better). OccuPy may also work poorly where the map has been post-processed or altered by machine-learning, sharpening, or manual alterations. It has been designed to work in a classification setting, and as such does not require half-maps, a resolution estimate, or solvent mask. It will likely benefit if you are able to supply these things, but does not need it.

Installation

OccuPy can be installed from the Python Package Index (PyPI)

pip3 install occupy

Usage

OccuPy is a command-line tool

$ OccuPy --help

 Usage: OccuPy [OPTIONS]                                                                                                                                              
                                                                                                                                                                      
 OccuPy takes a cryo-EM reconstruction produced by averaging and estimates a self-normative local map scaling. It can also locally alter confident partial            
 occupancies.                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                      
╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --input-map           -i                         TEXT     Map to estimate [.mrc NxNxN] [default: None]                                                             │
│ --output_map          -o                         TEXT     Output map name [default: out_<input_file_name>]                                                         │
│ --resolution          -r                         TEXT     Resolution of input map [default: None]                                                                  │
│ --amplify             -a                                  Alter partial occupancies, to make more or less equal to full occupancy?                                 │
│ --amplify_amount      -am                        FLOAT    How to alter confident partial occupancies [-1,1] [default: 1.0]                                         │
│ --amplify_limit       -al                        FLOAT    Hard limit below which map scale/occupancy will be considered unreliable for amplification               │
│                                                           [default: 0.05]                                                                                          │
│ --exclude-solvent          --retain-solvent               Should Estimated solvent be eliminated [flattened to 0]? [default: retain-solvent]                       │
│ --plot                     --no-plot                      Plot a histogram showing solvent model fit and occupancy confidence? [default: no-plot]                  │
│ --lowpass-input                                  FLOAT    Low-pass filter the input map to this resoution prior to scale estimation. Internal default is           │
│                                                           6*pixel-size. [Å]                                                                                        │
│                                                           [default: None]                                                                                          │
│ --lowpass-amplified                              FLOAT    Optionally low-pass filter the amplified output to this resolution [Å] [default: None]                   │
│ --kernel-size                                    INTEGER  Size of the local occupancy estimation kernel [pixels] [default: None]                                   │
│ --hedge-confidence                               INTEGER  Exponent order for confidence estimation, such that values > 1 are more careful when amplifying low      │
│                                                           occupancies                                                                                              │
│                                                           [default: None]                                                                                          │
│ --solvent-def                                    TEXT     Mask that defines non-solvent, used to aid solvent model fitting. [.mrc NxNxN] [default: None]           │
│ --save-all-maps            --no-save-all-maps             Save all maps used internally [default: no-save-all-maps]                                                │
│ --save-chimerax            --no-save-chimerax             Write a .cxc file that can be opened by chimeraX to show colored input/output maps                       │
│                                                           [default: save-chimerax]                                                                                 │
│ --min-vis-scale                                  FLOAT    Lower limit of map scale (occupancy) in chimeraX coloring & color-key [default: 0.2]                     │
│ --verbose                  --quiet                        Let me know what is going on [default: quiet]                                                            │
│ --relion-classes                                 TEXT     File of classes to diversify by occupancy amplification [_model.star] [default: None]                    │
│ --version                                                 Print version info and exit                                                                              │
│ --install-completion                                      Install completion for the current shell.                                                                │
│ --show-completion                                         Show completion for the current shell, to copy it or customize the installation.                         │
│ --help                                                    Show this message and exit.                                                                              │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

but the tools used within it are available from within a python environment as well

In[1]:
import occupy

In[2]: occupy.occupancy.get_map_scale?

Signature:
occupy.occupancy.get_map_scale(
    data: numpy.ndarray,
occ_kernel: numpy.ndarray,
sol_mask: numpy.ndarray = None,
                          sol_threshold: float = None,
                                                 save_occ_map: bool = False,
                                                                      verbose: bool = True,
)

Examples of use

In its basic form, OccuPy simply estimates the map scale, writes it out along with a chimeraX-command script to visualise the results easily

$ OccuPy -i map.mrc 
$ ls  
map.mrc    scale_map.mrc    chimX_map.cxc

To equalise all confident occupancies, use --amplify. Becuase you are manipulating the input image and not just estimating properties of it, there is now an output map as well.

$ OccuPy -i map.mrc -o no_solvent.mrc --amplify 
$ ls  
map.mrc    scale_map.mrc    out_map.mrc    chimX_map.cxc

To supress (flatten) solvent content use --exclude-solvent

$ OccuPy -i map.mrc -o no_solvent.mrc --exclude-solvent