Fig. 3: Residue environment distances from retinal measured using PyMol and LigPlot software, respectively.
From: Ultrafast structural changes direct the first molecular events of vision
a,c,e, The two rhodopsin models after 1 ps (yellow) and 100 ps (green) of photoactivation were superimposed in PyMol with the rhodopsin dark-state model (red) and the residue environment distances were drawn with a cut-off at 3.7 Å using dashed lines from the retinal in the dark (a) and after 1 ps (c) and 100 ps (e) photoactivation. The salt bridge between the Schiff base (SB) and counterion Glu113 is marked in cyan. The yellow-circled numbers 1 and 2 show the regions in which interactions will weaken and appear, respectively (see also the blue arrows). b,d,f, While PyMol displays the three-dimensional structure of amino acids in the previous panels, the LigPlot58 represents a flat interaction plot with all amino acids involved (orange) or less (grey) in the conformational changes during the picosecond time delays of photoactivation (dark (b), 1 ps (d) and 100 ps (f)).
