Alessandro, MAXRES is maximal number of residues. It's hardcoded in a binary. It is very likely that your alignment is not optimal, so you are trying to bring close regions that might be far away in space, but close in your bad alignment, or other way around. Best, Bozidar > I'm try to compare different structures found by a seqsearch.top script with a > compare.top script based on the compare.top present in one of the tutorials, > but I get an error that look like this: > pntdp___E> Increase MAXRES or gap penalities. > Wat does MAXRES do and how can I eventually increase it? > Thank you all > Alessandro