Update README.md

Fix link and point to #171

docs/demo/README.md

@@ -18,9 +18,9 @@ Gevokizumab inhibits the activity of interleukin-1β.
 3. Goto Antibody-antigen scenario page
 4. For antibody
 5. Upload `./input/4G6K.pdb` file
-6. Select chain H
+6. Select chain `H`. (In the haddock3 cli tutorial the H and L chain are merged to chain A, here we just use chain H, see #171)
 7. Import active residues: `31,32,33,34,35,52,54,55,56,100,101,102,103,104,105,106,1031,1032,1049,1050,1053,1091,1092,1093,1094,1096`,
-  these residues are the highly variable loops of the antibody also known as the paratope aka the region that binds the antigen. Residues predicted with [ProABC-2](https://github.com/haddocking/proabc-2), a deep learning framework to predict antibody paratope residues.
+  these residues are the highly variable loops of the antibody also known as the paratope aka the region that binds the antigen. Residues predicted with [ProABC-2](https://github.com/haddocking/proabc-2), a deep learning framework to predict antibody paratope residues. 
 8. For antigen
    1. Upload `./input/4I1B.pdb`
    2. Import active residues: `72,73,74,75,81,83,84,89,90,92,94,96,97,98,115,116,117`, these residues are the NMR-identified epitope residues of the antigen (table 5 of https://dx.doi.org/10.1016/j.jmb.2012.09.021). The epitope is the region that binds to an antibody.
@@ -106,6 +106,8 @@ CAPRI is a community wide yearly benchmark for docking methods.
 
 To zoom in on a chart, select it in the pulldown.
 
+If you found looking at the results that you want use a slightly different workflow, for example with different molecules, you can edit the job and resubmit it.
+
 ### Browse page
 
 The browse page shows the output of all the modules.
@@ -135,20 +137,6 @@ By clicking on yellow triangle of the contactmap module to see the report.
 
 Shows per cluster how chain A and B are likely contacting each other.
 
-#### Alascan report
-
-This module is not part of the antibody-antigen scenario. It is part of the refine scenario, which can be run with https://github.com/haddocking/haddock3/blob/main/examples/docking-protein-protein/data/e2a-hpr_1GGR.pdb as molecules and reference structure input. 
-
-This input will show for residue what the impact of a mutation would be.
-
-[![Screenshot of cluster bar graph of alascan report](./screenshots/alascan-cluster.png)](./screenshots/alascan-cluster.png)
-
-Also shows the energy difference between the wild type and the mutant for each structure.
-
-[![Screenshot of structure of alascan report](./screenshots/alascan-structure.png)](./screenshots/alascan-structure.png)
-
-Module will mutate the interface residues and calculate the energy differences between the wild type and the mutant, thus providing a measure of the impact of such mutation.
-
 #### Cluster report
 
 By clicking on chart icon of the 07 clustfcc module to see the report.
@@ -159,11 +147,19 @@ Plot of distance matrix, you can see the 11 clusters from the report page back h
 
 Any reports generated by haddock3 cli can also be shown in the webapp in a new window.
 
-#### Edit
+#### Alascan report
+
+This module is not part of the antibody-antigen scenario. It is part of the refine scenario, which can be run with https://github.com/haddocking/haddock3/blob/main/examples/refine-complex/data/e2a-hpr_1GGR.pdb as molecules and reference structure input. 
+
+This input will show for residue what the impact of a mutation would be.
+
+[![Screenshot of cluster bar graph of alascan report](./screenshots/alascan-cluster.png)](./screenshots/alascan-cluster.png)
+
+Also shows the energy difference between the wild type and the mutant for each structure.
 
-If you found looking at the results that you want use a slightly different workflow, you can edit the job and resubmit it.
+[![Screenshot of structure of alascan report](./screenshots/alascan-structure.png)](./screenshots/alascan-structure.png)
 
-An uploadied completed job can not be edited. So use an actual locally run job if you want to show that off.
+Module will mutate the interface residues and calculate the energy differences between the wild type and the mutant, thus providing a measure of the impact of such mutation.
 
 ## Talking points