Hi there,
maybe the subject is a little bit misleading but i couldn’t find any better
description. Basically I am trying to align two PDB structures, one is from the
PDB directly and the other one is a file containing conformation information
about a specific loop of the protein from the PDB. So I try to align this loop
to the residues 211-220 of the PDB structures. My commands go like this:
fetch 1g68
load loop.pdb
align 1g68 and chain A and n. CA+N+O+C and i. 211-220, loop
instead of aligning on the 40 atoms as expected I align solely on 8, which are
the N atoms. If I change the n. selection to O for instance I get
ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?). This
is with the macports compiled version of pymol 1.7.7.2 and the PyMOLX11Hybrid
1.7.4. However, doing exactly the same in the Macpymol version 1.7.4 it works
as expected. To even make it more weird if I use Python:
import __main__
__main__.pymol_argv = [ 'pymol', ‘-qc'] # Quiet and no GUI -qc
import pymol
pymol.cmd.fetch('1g68’)
pymol.cmd.load('loop.pdb’)
pymol.cmd.align('loop', ‘1g68 and chain A and n. N+CA+O+C and i. 211-220,
quiet=0)
it works as well. Does anybody understands what is happening here?
Thank you very much,
Max
PS: If you need the PDB files let me know. I don’t know if this list acceptes
files
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