Actually I have a problem in how to connect two portions of a protein...I have both, 2 pdb files for these portions and also a list of torsion angles. the problem is how to know the coordinate of the last atom in the first portion to be then joined to the second portion if u just can modify a particular phi and psi angles...recall that the second portion should not be moved, for example, I can just modify phi and psi angles of residue number 5 in the first portion to rotate it to be in the closest point (it's C carbon atom) to the second portion (it's N atom) then join them.... and as we all know that all these stuffs in 3D... so wht I need is how to calculate the coordinates of this last C carbon residue in the first portion.
thank u all in advance

Kamal

Your question does not pertain to Rosetta@home, so do not be surprised if no answer is posted.

---

Rosetta Moderator: Mod.Sense

Thank u...

But I think guys who work on Rosetta know or should know how it works...I think it also join portions of protein using phi and psi angles...but my question concerns on deep details beyond just put the portions after each others...

Kamal

Kamal, if you want to build some missing density between two portions of a protein using phi/psi angles, the second half will generall move relative to the first half, unless you idealize all the backbone torsions firts. Hope that helps.

---