show generated figure

Author: thorstenwagner

README.md

@@ -5,11 +5,11 @@ PyMissense create the plot and modified pdb as shown in the [AlphaMissense paper
 
 AlphaMissense allows you to identify regions in your amino acid chain that are critical for protein function. This notebook does two things:
 
-1. It generates a plot similar to Figure 3d of the [AlphaMissense paper](https://www.science.org/doi/10.1126/science.adg7492)
+1. It generates a plot similar to [Figure 3D](https://www.science.org/doi/10.1126/science.adg7492#F3) of the [AlphaMissense paper](https://www.science.org/doi/10.1126/science.adg7492)
 
-    ![Alt text](resources/img/fig3d.png)
+    ![Alt text](resources/img/3d.png)
 
-2. It creates a modified PDB file where the temperature factor is replaced by the pathogencity predicted by AlphaMissense that allows you to visualize the effect with Chimerax, like Figure 3f of the paper:
+2. It creates a modified PDB file where the temperature factor is replaced by the pathogencity predicted by AlphaMissense that allows you to visualize the effect with Chimerax, like [Figure 3F](https://www.science.org/doi/10.1126/science.adg7492#F3) of the paper:
 
     ![Alt text](resources/img/fig3f.png)
 
@@ -41,7 +41,7 @@ options:
 
 You can provide the positional argumetn `--pdbpath` if you want to use an experimental PDB, otherwise it will instead download the alphafold predicted PDB. One example could be:
 
-For example, to reproduce Figure 3D (the middle one) and the generate the PDB shown in Figure 3F do:
+For example, to reproduce [Figure 3D](https://www.science.org/doi/10.1126/science.adg7492#F3) (the middle one) and the generate the PDB shown in [Figure 3F](https://www.science.org/doi/10.1126/science.adg7492#F3) do:
 
 ```
 pymissense Q9UQ13 out --maxacid 200