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In this case, skip the opening by using the default radius value of 0. Small artificial objects will be removed by inverse hole filling.
A peak search is then performed, and the density inside a sphere (default radius 0.7 Å) about each peak is summed.
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Description Unit Value N number of channels 30, 50 R default service radius m 120, 180 unit area π m2 25 number of WSAPs per [0.025 0.02525 : 0.05] density of WSAPs (=m/A) [0.001 0.02] duty cycle 1.0 min session duration time sec 120 max session duration time sec 2400 mean session duration time sec 333 session termination rate 10.8.
We used a simple van der Waals surface for the protein and the programme default probe radius of 1.15 Å.
The putative binding cavity of p62 ZZ-domain was predicted using Fast Connolly Type implemented in the MOLCAD module in SYBYL-X 1.3 by a similar protocol as described previously65, before which the corresponding ZZ domain residues were first selected to generate a protocol with the default threshold radius of 0.5.
The solvent-exposed residues were identified using the cutoff value of ≥30% for the relative surface accessibility area of the side chain in Swiss-PDB Viewer[52] using the default probe radius.
Asymptotic Axes Chart: Set Power to 3. Reset the axes to defaults if Radius = 1 and Factor =.5 while Power = 3.
The separation between the detected sources and the input coordinates are provided in the sepn (separation) column in the same units at the radius (default is arcmin).
All remaining gap spheres exceeding a minimal predefined radius (default is 1.0 Å) are denoted as "final spheres" and used to define surface pockets and cavities (Figure 1). Figure 1 Two-dimensional depiction of the pocket detection process of SURFNET.
Organisms within a certain radius (default 2) of an empty position compete to reproduce into that position using probabilistic fitness-based selection.
Using the default outer probe radius of 10 Å in the 3V server (http://3vee.molmovdb.org/), we could not detect any internal cavity in influenza B virus HA.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com