Cavity programs: Difference between revisions
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==MOLEonline== | ==MOLEonline== | ||
[https://mole.upol.cz/ MOLEonline]<ref name="moleonline">PMID: 29718451</ref> locates and characterizes channels, tunnels and pores. Visualization in LiteMol, which has many menu options for rendering, but does not offer transparency. The thin "C-α trace" is the least obscuring. | [https://mole.upol.cz/ MOLEonline]<ref name="moleonline">PMID: 29718451</ref> locates and characterizes channels, tunnels and pores. Visualization in LiteMol, which has many menu options for rendering, but does not offer transparency. The thin "C-α trace" is the least obscuring. One can specify ''starting points'' and ''end points'' by selections, residue lists, or XYZ points. | ||
Personal experience: When SARS-CoV-2 spike protein [[6zgi]] is submitted, cavities (connecting to the surface) and voids were displayed automatically. None represented the membrane-proximal cavity. When the center of the deepest part of the membrane-proximal cavity was specified via XYZ (215.6, 215.6, 157.6), ''tunnels'' were detected, including the three pictured at right. | |||
==PACUPP== | ==PACUPP== | ||
