Re: [modeller_usage] RMSD

[Modeller Caretaker <>]

Mathew Smith wrote:
> I would like to measure the rmsd between the secondary structure elements of my
> models and the templates.
> I have been trying to do this using the selection.superpose method, as shown in
> the example file examples/commands/pick_atoms.py, to select a range of
> residues. But it keeps giving the following error:
...
> KeyError: 'No such residue: 4'
>
> I have only been programming for a few months and can't see why it is giving
> this KeyError?

Like it says, there's no residue called "4" in your model. You should 
check your PDB file to make sure it's there! A common error is to forget 
the chain ID - if your residue is in chain A, you need to specify this, e.g.

s = selection(mdl.residue_range('4:A', '10:A'))

If in doubt, you could add a little loop to print all the residues with 
something like:

for r in mdl.residues:
    print r


	Ben Webb, Modeller Caretaker
--
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