On Jan 20, 2015, at 3:34 PM, Alejandro Virrueta <alejandro.virrueta@yale.edu> wrote:

Hello all,

Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example?

Hi Alex, It's a little ugly but very possible. The treatment of alt locs in Chimera 2 will be less arcane, but Chimera 1 is all there is right now. Anyway, You can get the atoms involved in a particular chi angle by using the "chiAtoms" function: from chimera.phipsi import chiAtoms chiExemplar = chiAtoms(res, 2) # for chi2 Now, these are just the first atoms in the residue, usually alt loc A (or blank, for residues with no alt locs). To find the corresponding B alt loc atoms, you will have to rummage through the residue: bAtoms = [] for ce in chiExemplar: for a in res.atomsMap[ce.name]: if a.altLoc == 'B': bAtoms.append(a) break else: raise AssertionError("No B alt loc for atom %s" % ce.name) Then finally you can compute the chi angle: from chimera import dihedral chi = dihedral(*[a.coord() for a in bAtoms]) Like I said, a little ugly, but doable. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu