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Hi Morten,<br>
<br>
your example does not include symmetry. You can see the
implementation of <br>
<br>
iotbx.show_distances 1yjp.pdb<br>
<br>
that computes all-vs-all distances in most efficient way and also is
symmetry-smart.<br>
<br>
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).<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/18/15 11:30 AM, Morten Gr�ftehauge
wrote:<br>
</div>
<blockquote
cite="mid:CAEAG6YQsmapOrhj4inqvESf=wtbJFrfXMaCGMiq35pd_FZZfzg@mail.gmail.com"
type="cite">
<div dir="ltr">Hi everyone,�
<div><br>
</div>
<div>I'm trying to do some distance extraction of hetero atoms
in pdbs. I've got�</div>
<div><br>
</div>
<div>
<div><font face="monospace, monospace">� � for model in
pdb_obj.hierarchy.models():</font></div>
<div><font face="monospace, monospace">� � � for chain in
model.chains():</font></div>
<div><font face="monospace, monospace">� � � � for rg in
chain.residue_groups():</font></div>
<div><font face="monospace, monospace">� � � � � for ag in
rg.atom_groups():</font></div>
<div><font face="monospace, monospace">� � � � � � for atom in
ag.atoms():</font></div>
<div><font face="monospace, monospace">� � � � � � � if
atom.hetero == True:</font></div>
<div><font face="monospace, monospace">� � � � � � � � print
�atom.distance(atom)</font></div>
<div><br>
</div>
</div>
<div>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).�</div>
<div><br>
</div>
<div><br>
</div>
<div>I also noticed something weird in this tutorial:�</div>
<div><a moz-do-not-send="true"
href="http://cctbx.sourceforge.net/sbgrid2008/tutorial.html">http://cctbx.sourceforge.net/sbgrid2008/tutorial.html</a><br>
</div>
<div>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).�</div>
<div><br>
</div>
<div>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?).�</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Morten�</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</blockquote>
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