[Chimera-users] Alternate conformations in residues
pett at cgl.ucsf.edu
Wed Jan 21 13:31:33 PST 2015
On Jan 20, 2015, at 3:34 PM, Alejandro Virrueta <alejandro.virrueta at 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?
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':
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.
UCSF Computer Graphics Lab
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