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This section contains help on common concerns and questions. Further help and insight is offered through the issue tracker.

Command-line help

For brief information regarding input options on the command line, please use 

$ occupy --help
For extensive information regarding input options, see the GUI overview tutorial.

The modified map is similar to the input map

  1. The modification is effected by the power you choose, where values larger than 1 mean to modify. Larger values mean to modify more, and typically values between 2 and 10 are useful. Try increasing it.
  2. Check your solvent model (tab next to output log). The modification is suppressed if the estimated solvent model is very wide, which decreases confidence in partial occupancies. If
  3. there isn't enough solvent for the fitting of the solvent model, it will typically be too wide and prevent modification of lower-scale components. You can check this by using the --plot option and inspecting the output. You can also use --solvent-def <mask.mrc> where the mask is a conventional solvent-mask. This will allow these regions to be omitted during solvent fitting. This mask does not need to be perfect, and does not limit the modification to areas inside it.

The estimated scale is just 1 everywhere

  1. Well you might have a rock of a complex.
  2. If you set the value of --tau/-t manually low, then this is the reason. If it got auto-calculated low, you can increase it, but this is a bad idea. It is rather better to increase the --kernel so that the value of tau is automatically increased. You may also waent to increase --lowpass/-lp ot increase the number of sampled pixel nv. You can see what paramters were calculated and used by checking the output log file or using the --verbose option. Increasing the kernel size and/or lowpass setting permits more confident sampling of the local scale, but does increase the granularity. Usually a kernel size of 5 or 7 is adequate, with nv-values in the range 30-100. Low-pass defaults to 8 or 3*pixel-size, which ever is larger, but depending on resolution and pixel-size this may be adjusted depending on the sought granularity.
  3. OccuPy puts everything on a scale based on what it estimates as "full" through a non-exhaustive search. It is non-exhaustive because it's much faster. If the "full" scale is under-estimated, lots of regions will be "over-full", i.e. over-estimated as full. YOu can reduce the --tile-size from its default value 12 to reduce the area of what defines "full" scale, which will narrow the definition and in general increase the value of full occupancy, thus stretching the range of the estimated scale. For high-resolution maps, a very small tile-size makes the local scale approximate the mass of individual atoms.

There is a sphere of noise surrounding the amplified map

  1. If the confidence is over-estimated, low-scale components will be permitted to be amplified. You can hedge the confidence by using --hedge-confidence <val>, where <val> is a power, meaning that higher values hedge more. 10 is a reasonable value to try.
  2. Another possible reason for the confidence being over-estimated is that the solvent model mean and/or variance is under-estimated. A typical reason for this is that the solvent has been flattened, such that the solvent is not gaussian. OccuPy was not designed for this type of reconstruction, since such flattening is typically enforced using a mask which has thus already delineated solvent vs non-solvent.
  3. If the map is not solvent-flattened, and confidence-hedging does not alleviate solvent-amplification surrounding the main map component, use --solvent-def <mask.mrc> where the mask is a conventional solvent-mask. This will allow these regions to be omitted during solvent fitting. This mask does not need to be perfect, and does not limit the modification to areas inside it.

The estimated scale looks like my local resolution

OccuPy estimates the scale. The scale decreases due to both lower resolution and lower occupancy. Since it is not possible to trivially separate these factors, the current approach to estimate occupancy as separate from lower resolution is to low-pass filter the input before estimating the local scale. This is turned on
when amplifying or attenuating the map, to minimize over-amplification of low-scale components that are simply low resolution. If one is just estimating scale, but still wants to reduce resolution-dependent effects, the low-pass filtration before scale-estimation can be used. It should then be combined a low-pass filter to specify the worst resolution among the components for which occupancy is to be estimated. For membrane proteins, see here.

My membrane or detergent looks funny

Membranes are lower in resolution due to their amorphous nature which cannot be coherently averaged. Because this reduces the local scale, membranes are estimated at low scale. The estimated scale of membranes are thus not a measure of relative density or occupancy. The low-pass filtration intended to reduce influence of resolution-dependent scale factors is only an approximate measure, so that the precise meaning of the local scale of membrane and another amorphous regions (as estimated by OccuPy) is not well-defined. The lower scale generally reflects intuition however, and permits weak attenuation to de-emphasize these regions to make visualization easier.