Hi everybody. I am working on a project: the final aim is to do molecular dynamics simulations of a sodium channel. First I have to build the model using homology modeling. I used HHpred and Modeller but I have to go back to the alignment to check if everything is all right since the final model contains loops that will not be simulated. I am new to bioinformatics and all these stuff so I need a little bit of help. Since the protein is big (2016 aa), I need to check the alignment (4 templates + query sequence) domain by domain (4 in total) or even segment by segment (6 for each domain). The question is: is there any tutorial on how to do this? I really do not know where to start from. I can look at the MSA but for me it does not say anything! Thank you.
