 That does not mean that homology modelism is entirely trivial though. Remember quality of the alignment. What if I had two sequences here and I just happened to screw up a little bit so I offset them by one amino acid? That can't be the end of the world, right? It's just one amino acid. The problem is that this is going to slide everything in the secondary structure elements. I'm going to take a helix and literally turn the entire helix one third of a turn. Those two helixes have an RMST of 3.8 angstrom. It's a gigantic error. Remember what I told you before? Two angstrom structures are good. We can frequently get that with homology modeling. Around five old bets are off so two angstrom error might not sound like insanely good but it's less than half of having one helix having made a single offset in the sequence alignment. This stresses another part with homology modeling. We need something that is close to us. The higher the sequence, even if we know that two sequences are homologous, the higher the sequence identity, the better I will be able to align them. The quality of the alignment and the fraction of the sequence identity is really going to be the most deciding factors for how good your homology models will be in the end. Sure, then it's great if you have a wonderful way of placing the amino acid side chains but it's not at all going to be important as the alignment. In practice, we don't do homology modeling manually anymore. Whenever I need to do something, I would go to one of a couple of websites. I happen to love Johannes Söding's websites called HH Pred. They're using some hidden mark of model method exactly what is not important. Most, in most cases, you don't need to know the entire internal machinery just to create a homology model. You can just paste your sequence in a window, click through, look at the multiple sequence alignment and then they will gradually take you through step by step until you have a pdp file you can download. It's stellar. Another alternative is Torsten Schwede. They have a site and program actually for Windows that you can download called Swiss model. Here too, you can just input your sequence and I think even from the Windows program you can click a button and have this interactively upload your sequence, create a homology model for you and you will get the structure back. It's amazing work and again it has so many other things in bioinformatics. This is available for free. It has been fantastic for science.