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Hi,

Just curious if there is or there will be a flag to use Roland's 2010 Rotamer library within Rosetta. We have been replacing the 2008 binaries with data using the 2010 library and then using the 2008 flag, which works well enough. I'm still learning C++, or I would try and implement it myself.

Also, if it does already work within Rosetta, where would I find it within the code, and which level of smoothing was used? (optim, 5%, 20%)? We have been using optim (with the neighbor-dependent ramachandran flag) across most of Rosetta's apps and it seems to work well.

hi,

is it possible to restrict a space in Rosetta Design... like use some dummies guaranteeing that positions in this area are not to large thus blocking space... or do I have to restrict the surrounding amino acids going for small ones and just hope that´s enough.
Thanx!

Hi, fellows:
We have two transmembrane peptide from two separate membrane proteins and we would like to see how they pack. The conformation of helix 1, i.e., tilt angle w.r.t the membrane etc, is determined by NMR. For the second helix, we currently take it as an ideal helix. The tilt angle for helix 2 is also known. This problem is similar to the glycophorin A packing problem addressed in "Toward high-resolution prediction and design of transmembrane helical protein structures".

Hi,

does anybody have experience or ideas on how to involve waters in a packing/design process?
I want to repack a protein but want to make sure to include some water filled cavities. Is there a way to define waters or a sort of placeholder, though explicite waters would be better, so that the design-packer can generate a suitable surrounding.
Thanks!