Reply To: Minimization Toolkit W/GUI

[Anonymous]

Hi Jared,

Many thanks for your prompt response. I tried the new GUI and I have some more comments/questions:

1. Loops at the N- and C-term cannot be relaxed, perhaps because PyRosetta introduces a cut point and tries to join the two ends as in the internal loops (see attached files Nterm_relax.txt and Cterm_relax.txt). Is there any workaround for this?

2. I selected to optimize the rotamers of two internal loops which I modeled with MODELLER, but instead the program also optimized rotamers far from the selected loops.

3. Upon optimization I tried to relax the two loops by setting the minimization slide-bar to 1 and dfpTolerance to 0.50. I created 10 decoys. All of them were “broken” at the cut point of loop2 and only one had an intact loop1. What am I missing here?

4. Could you please explain the difference between Relaxation and Minimization, cause it seems I have confused these two terms. I had the notion that the latter allows more drastic changes to the structure.

5. Which parameter of Rosetta does dfpTolerance refer to (minimize_set_tolerance, stringent_relax, use_abs_tolerance) ? What does the “Minimization” slide-bar control?

I’m sorry for asking so many questions, I don’t mean to waste your time. Some short answers and pointers to the documentation would be much appreciated!

thanks in advance,
Thomas

PS: I’m leaving for a workshop on Monday, so I might be slow in my responses.