Focus Documentation

Common Image Processing

is the resolution limit that should be applied during the image processing, in Angstroem. If for example you are processing a negative stain image, than usually you would want to limit the included resolution to “16.0” Angstroem, since there is little chance that any information beyond that resolution can be found in the image. Limiting the resolution to reasonable numbers allows to better do the unbending because less noise is included during the localization of the CCMap's peaks. The data in the end are evaluated without any resolution limitation. So, limiting the resolution here does not mean that higher resolution data will not be available. However, if the reference did not contain reference details beyond the here specified resolution, then the unbending has a hard time to follow structural details at highest resolution. It is therefore recommended to set the resolution limitation to a value that is optimistic but not ridiculously high.

is a limit that is used to cutoff the low-resolution artifacts. When looking at a high-resolution 3D map, sometimes alpha helices are easier to identify when the low-resolution components are not included in the dataset. Usually, you can keep this value at “200.0” Angstroem.

This switch allows you to determine if a global fixed resolution limit (specified here in the 2dx_merge program) should be applied to all images during merging, or if every image should rather be merged with its own individually defined resolution limit.

Specifies the resolution up to which the merged dataset can/should be used as reference for unbending of the images. The other parameter “RESMAX - Upper Resolution Limit” is used to define the resolution limit up to which the processing of one image, or up to which the merging of all available data should be done. This parameter here “MergeResolution - Resolution of the merged dataset” instead defines, to which resolution the final merged dataset should be limited, to be used as reference. You could for example process data up to 7A resolution, but provide a reference that only contains data up to 10A resolution, so that more noisy data in the 10-7A range are not used to wrongly influence the re-processing of your images.

is the assumed vertical dimension of the 2D crystal in 3D space. A normal membrane protein crystal would have a vertical thickness of 100.0 Angstroems, so that a vertical slab dimension of “200.0” Angstroem should be enough to include the entire 3D volume.

Plot generation

can be used to increase the high-resolution details in the final map. A negative temperature factor of -100 Ångstroem-2 for example enhances higher resolution components, using a quadratic profile, upto the RESMAX cutoff.