Hi Max,
If you send me the loop.pdb file then I'll have a look at the issue.
Cheers,
Thomas
On 23 Feb 2016, at 09:03, Ebert Maximilian <m.eb...@umontreal.ca> wrote:
> 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
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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