from pymol import cmd, stored def surfaceatoms (molecule" NIL"show True, verbose True, cutoff 2. 5): " " " surfaceatoms finds those residues on the surface of a protein that have at least 'cutoff' exposed A2 surface area. PyMOL can display labels for atoms, residues etc.but they are almost worthless for publications. My recommendation is to add them on the final image using MS Powerpoint or any painting software.
PyMol Exercise F: A simple animation within PyMol, and for PowerPoint PyMol Exercise G: Harnessing the power of PyMol: introducing scripts PyMol Exercise H: Select command, parameters, scripting, and subsets. DRAFT CHAPTER OF THE OFFICIAL PyMOL MANUAL (For PyMOL Sponsors) A new installment This chapter is part of a comprehensive manualinprogress, so To run any text command, type it in at a PyMOL command line and hit [Enter.
Getting started: explore a protein PyMOL is great for casual visualization of biological molecules. Unlike most scientific software, PyMOL is highly polished; it wont unexpectedly crash while youre using it.
PyMOL can produce highquality graphics, on par with Molscript, without needing to manually edit text files. PyMOL has an extensive help system, and documentation can be found by typing help command for many commands.
PyMOL color blue, akeeper# Residues numbered 110, # which were collected in# the named selection" akeeper, " # are colored blue. PyMOL color red, ss h# The representations of# helical residues# are colored red. Identifying atoms or residues on the screen.
To show the identity of an atom, double click with the left button on any point in the molecule. This brings up a menu that allows you to do various actions to the atom, residue, chain or