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