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I agree with Phil about UNK - it seems to be good indeed to call
unknown (undefined) residue as it appears on the map rather than
call ALA something that in fact is TYR, and then later on getting
confused about the mismatch between actual sequence and the one
derived from PDB file. This is actually what I get confused all the
time looking at results of model building programs, because the
first thing I always do is I compare the real actual sequence with
the one derived from PDB file - just to validate the result of model
building.<br>
<br>
However, I agree with Tom too about loosing identity in cases where
we really do know what to expect: polypeptide or rna/dna.<br>
<br>
Hm... interesting situation -:)<br>
<br>
I guess UNK is may be still better, ONLY IF you go one level deeper
and look at atom names (or make sure you do that consistently). Say
you name a "residue" as UNK and name corresponding atoms within this
residue as CA, N, C, O (kind of peptide pattern) - then you have a
chance to guess what it is. Of course how you then know where you
place those CA,N,C and O...<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 7/28/10 3:19 PM, Tom Terwilliger wrote:
<blockquote cite="mid:051EFF69-34F6-4F8D-B9B5-C47DB38DF393@lanl.gov"
type="cite">One disadvantage of using UNK is that it is often a
loss of information. For example in the case Phil mentions...we do
think that we have a polypeptide. By labelling protein residues
UNK we no longer distinguish them from DNA, or depending on HETATM
vs ATOM identification, from ligands.
<div>-Tom T</div>
<div><br>
<div>
<div>On Jul 28, 2010, at 4:01 PM, Phil Evans wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>UNK residues have another valid use where you can see
peptide but not assign a sequence register. A poly-Ala
model in that case is better labelled UNK than ALA, since
it isn't ALA<br>
<br>
Phil <br>
<br>
<br>
On 28 Jul 2010, at 19:12, Pavel Afonine wrote:<br>
<br>
<blockquote type="cite">Dear Ed,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">I think it is very important to
be able to include unknown atoms<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">in a deposited pdb file (with
echoing the caveat about flooding<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">the structure with UNK's to
lower the R-factor).<br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">yes, as I wrote in original reply,
including these atoms may improve the map and in turn
may reveal or improve some its other important
(biologically) places. The only point is: please define
these dummy atoms properly, providing all the
information, such as scattering element type that you or
your program used for such an approximation.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">For one thing, these structures
are produced not just for structure-factor<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">calculation and validation. Many
of the end users will never even<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">bother to do a structure factor
calculation.<br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">The ability to reproduce the
R-factor is not only for someones pleasure but for the
validation purposes at least. If I've got a PDB file for
which I can't compute the R-factors (and, by the way,
even the map too), then I don't need the deposited Fobs
too, unless I'm going to re-determine the structure from
scratch.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">It important for the<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">depositor to be able to refer to
an unknown but likely significant<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">ligand and for the reader to be
able to go and look at that position<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">(ideally surrounded by electron
density).<br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Sure, it is important.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">For another thing, the structure
factor calculation will give exactly<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">the same result whether the
dummy atoms are omitted or are flagged<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">with zero occupancy or atom-type
X to be ignored in sf calculation.<br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">If you look in PDB you will find
that very often the occupancies are not set up to 1.
Plus, as I mentioned, often the B-factors for these
atoms are set to some funny numbers (looks like they
were refined).<br>
</blockquote>
<blockquote type="cite">Are we sure that these programs
were ignoring these dummies in Fcalc calculations? If so
how the B-factor were refined, or they were made up?<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Again, if it is defined properly,
for example, like this:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">ATOM 1959 O DUM A 1
-8.762 8.060 25.324 1.00 31.23 O<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">or<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">ATOM 1959 O UNK A 1
-8.762 8.060 25.324 1.00 31.23 O<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">then it is absolutely OK to have
such entries, because it is completely defined and can
be used in any calculations without any unnecessary
guesswork. But if you start masking things with X or
blanks then I (and the software I write) will start
asking all these nasty questions...<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">All the best!<br>
</blockquote>
<blockquote type="cite">Pavel.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">_______________________________________________<br>
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<div><br>
Thomas C. Terwilliger<br>
Mail Stop M888<br>
Los Alamos National Laboratory<br>
Los Alamos, NM 87545<br>
<br>
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