[cctbxbb] Atom selections for distance (embarrassingly simple)

[Pavel Afonine]

Hi Morten,

your example does not include symmetry. You can see the implementation of

iotbx.show_distances 1yjp.pdb

that computes all-vs-all distances in most efficient way and also is 
symmetry-smart.

You can combine functionality of some pieces of iotbx.show_distances 
(those that give you indices of pairs) with the list of atoms from 
pdb_hierarchy (that gives you all labels: residue names, atom names, etc).

Pavel

On 2/18/15 11:30 AM, Morten Grøftehauge wrote:
> Hi everyone,
>
> I'm trying to do some distance extraction of hetero atoms in pdbs. 
> I've got
>
>     for model in pdb_obj.hierarchy.models():
>       for chain in model.chains():
>         for rg in chain.residue_groups():
>           for ag in rg.atom_groups():
>             for atom in ag.atoms():
>               if atom.hetero == True:
>                 print  atom.distance(atom)
>
> Which prints out 0.0 as expected. But I can't figure out how to, say, 
> measure the distance to an atom in the previous residue (if there is a 
> previous residue).
>
>
> I also noticed something weird in this tutorial:
> http://cctbx.sourceforge.net/sbgrid2008/tutorial.html
> They truncate a non-standard amino acid to the beta-carbon but this 
> only works because there's an alternate conformation with a standard 
> amino acid (Cys). So it wouldn't work with a seleno-met for instance 
> (I know there's a convert-to-ala function in mmtbx - I said it was 
> weird, not terrible).
>
> Anyway, I hope someone can explain the distances thing for me. I'm 
> sure there are multiple ways of doing it (should I just do a selection 
> of "hetatm" and iterate over them and try to get some distanes?).
>
> Cheers,
> Morten
>
>
>
>
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