Hi bb, I have a question about TLS group assignment. I have a loop that is poorly ordered. The backbone can still mostly be built, though that's probably just the predominant conformation of many. TLSMD usually assigns a group border on one or both sides of this loop, though the assignment isn't always consistent. Given that I know the loop is poorly ordered, it might not be appropriate to allow it to share TLS parameters with the adjacent well-ordered regions. The way I see it, there are 3 options:
1. Allow the loop to continue to be integrated into a larger TLS group (probably not ideal) 2. Assign the loop it's own TLS group 3. Omit the loop from TLS assignment entirely (i.e. skip those residues in the .tlsin file) (2) seems the most reasonable to me, but introduces more parameters that probably aren't meaningful and may contribute to overfitting. On the other hand, I don't know if (3) is scientifically sound and/or will lead to problems refining in refmac. What would be my best option? Interested to hear thoughts on this, thanks! Shane Caldwell McGill University
