Re: [PyMOL] Problem aligning two structures: ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?)

[Thomas Holder]

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  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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[PyMOL] Problem aligning two structures: ExecutiveAlign-Error: atomic alignment failed (mismatched identifiers?)

[Ebert Maximilian]

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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