Data and code to create figures of "Rehybridization dynamics into the pericyclic minimum of an electrocyclic reaction imaged in real-time"

<p>Instruction of making Fig 4 in the main text:<br> 04/07/2023, SLAC, CA<br> Yusong (Liu), on behalf of Thomas (Wolf)</p> <p>1. Making Figure 1:<br> Figure 1 is fully vectorized with file &#39;Figure-1.svg&#39;, also saved in a png version, &#39;Figure-1.png&#39;</p> <p>2. Making Figure 2:<br> The data plots in panels a and b are produced from a Matlab script: &#39;MakingFig2MainText.m&#39;<br> This script loads data saved in &#39;TerpNatCommFig2.mat&#39; and produce several files if using the saving condition:<br> &#39;PDFStaticTwoDelaysExpSim_22.fig&#39;<br> &#39;PDFStaticTwoDelaysExpSim_22.png&#39;<br> &#39;PDFStaticTwoDelaysExpSim_22.svg&#39;<br> The final Figure 2, &#39;Figure-2.svg&#39;, then was assembled using &#39;PDFStaticTwoDelaysExpSim_22.svg&#39; and &#39;Molskeleton.svg&#39;.</p> <p>3. Making Figure 3:<br> The data plots in panels a, b, and c are produced from a Matlab script: &#39;MakingFig3MainText.m&#39;<br> This script loads data saved in &#39;TerpNatCommFig3.mat&#39; and produce several files if using the saving condition:<br> &#39;Fig3PDFFalseCMapLineOutExpSim_V10.fig&#39;<br> &#39;Fig3PDFFalseCMapLineOutExpSim_V10.png&#39;<br> &#39;Fig3PDFFalseCMapLineOutExpSim_V10.svg&#39;<br> The final Figure 3, &#39;Figure-3.svg&#39;, then was assembled using &#39;Fig3PDFFalseCMapLineOutExpSim_V10.svg&#39; and &#39;MolCartoonsFig3.svg&#39;.</p> <p>4. Making Figure 4:<br> (1). Drawing the signal in Fig. 4 panel a<br> Fig. 4a was generated from a py script: &#39;MakingFig4aMainText.ipynb&#39;<br> Run this script and it will load the data set &#39;MainFig4aData.npy&#39;generate a figure showing Fig. 4a.<br> Change the figure saving condition to decide whether or not save the figure to both .svg and .png files as below:<br> &#39;Figure-4a.png&#39;<br> &#39;Figure-4a.svg&#39;<br> (2). Drawing the signals in Fig. 4 panels b and c<br> These two panels, the signals are drew from a Matlab script: &#39;MakingFig4bcMainText.m&#39;<br> Run this script and it will load data set &#39;TerpNatCommFig4.mat&#39; and plot panels b and c<br> Change the figure saving conditions to decide whether or not save to both .svg and .png files as below:<br> &#39;Fig4DataPanelsbc_v11.fig&#39;<br> &#39;Fig4DataPanelsbc_v11.png&#39;<br> &#39;Fig4DataPanelsbc_v11.svg&#39;<br> (3). Fig 4 is then assembled with the 3 data plot panels, molecular cartoons, and equations:<br> Data plot panels:<br> &#39;Figure-4a.svg&#39;<br> &#39;Fig4DataPanelsbc_v11.svg&#39;<br> Molecular cartoons:<br> &#39;Fig4aCartoon.svg&#39; &#39;Fig4bCartoon.svg&#39; &#39;Fig4cCartoon.svg&#39;<br> And equations:<br> &#39;Fig4bEquPhi.svg&#39; &#39;Fig4cEquPsi.svg&#39;<br> Fig 4 is fully vectorized with file: &#39;Figure-4.svg&#39; and also saved as a .png version &#39;Figure-4.png&#39;</p> <p>5. Making Figure-5:<br> The whole Fig. 5 is produced from a single .py script: &#39;MakingFig5MainText.ipynb&#39;<br> Run the script and it will plot Figure-5. If choosing the save conditions, then it will save Figure-5 to &#39;Figure-5.svg&#39; and &#39;Figure-5.png&#39;.</p>