Rotkit: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
New Script
Forster-distance-calculator: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See DisplacementMap.
New Script
propka: Fetches the pka values for your protein from the propka server. propka generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
The iterate command executes a Python expression for all atoms in a selection. The local namespace exposes all atomic identifiers and properties as read-only Python variables. The global namespace by default is the pymol module namespace, and thus exposes objects like cmd and stored. The order of iteration is that of the internal atom ordering.
The alter command is equivalent to iterate, but ..→
