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Hi Pavel<br>
<br>
A bunch of extremely useful slides, thanks for making them available to
the world!<br>
<br>
Inevitably, though, given the nature of our field, there's one slide I
must challenge, the 2nd-last one of the validation pack, where you
recommend against the use of UNK atoms, but don't say why:<br>
<br>
<snip><br>
Some programs and people tend to interpret unknown density using “dummy<br>
atoms”. In PDB files it typically looks like this:<br>
ATOM 10 O UNK 2 6.348 -11.323 10.667 1.00 8.06 X<br>
ATOM 11 O UNK 2 6.994 -12.600 10.740 1.00 7.16 X<br>
ATOM 12 O UNK 2 6.028 -13.737 10.607 1.00 6.58 X<br>
ATOM 13 DUM UNK 2 6.796 -15.043 10.583 1.00 8.28<br>
ATOM 14 DUM UNK 2 5.099 -13.727 11.792 1.00 7.15<br>
- <b>Do not deposit this in PDB</b>, especially if chemical element
type is undefined<br>
(rightmost column)<br>
</snip><br>
<br>
<br>
Why should one not be allowed to indicate in the model that there was
very clear, atomic density whose chemistry nevertheless could not be
explained?<br>
<br>
The reason we group atoms into chemical entities is purely so we can
impose restraints on interatomic distances and thereby compensate for
the poor data-parameter ratio. But chemistry is not a substitute for
making /scientific/ sense of the model, that problem frequently lies
well beyond the reach of the model -- yet that should not stop the
model from being deposited, as would be the logical conclusion of your
recommendation. <br>
<br>
The scenario is universal, particularly acute in structural genomics
but possible even in ligand-binding studies. <br>
<br>
(Of course, if what you meant to say that UNK atoms are to be used
extremely judiciously, and it is *not* okay to flood a bad model with
UNK atoms only to get the R-factor down -- then I'm totally with you!) <br>
<br>
phx.<br>
<br>
<u>Full disclosure</u>: I am one of the culprits behind the JCSG
persuading the PDB to accept UNK as valid residue type, after we had
run into simply too many models where there was clearly something
bound, but no quick/cheap way of figuring out what it was.<br>
<br>
<br>
<br>
<br>
On 27/07/2010 20:43, Pavel Afonine wrote:
<blockquote cite="mid:4C4F36EC.90405@lbl.gov" type="cite"> Hi Everyone,
<br>
<br>
recently I had to update or do from scratch my talk "slides" on various
subjects such as crystallographic structure refinement, maps,
validation and some general PHENIX overview. Since I spent pretty
significant amount of time making all these "slides" , ... I was
thinking that may be this might be of use for some of you, so here it
is...
<br>
<br>
- 42 pages of general introduction to structure refinement:
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf">http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf</a>
<br>
<br>
- 45 pages of phenix.refine overview (including extended details about
its use from the command line):
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf">http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf</a>
<br>
<br>
- 42 pages of "Some Facts About Maps":
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/latest/pavel_maps.pdf">http://www.phenix-online.org/presentations/latest/pavel_maps.pdf</a>
<br>
<br>
- 50 pages of "Crystallographic Structure Validation":
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/latest/pavel_validation.pdf">http://www.phenix-online.org/presentations/latest/pavel_validation.pdf</a>
<br>
<br>
- 31 pages of introduction to PHENIX:
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/latest/pavel_phenix_intro.pdf">http://www.phenix-online.org/presentations/latest/pavel_phenix_intro.pdf</a>
<br>
<br>
Most of the slides in "Introduction to PHENIX" came from Paul Adams,
Tom Terwilliger and Nat Echols. Thanks Nat and Jeff Headd for providing
with interesting examples of structures with unusual geometry.
<br>
<br>
All the best!
<br>
Pavel.
<br>
<br>
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<br>
</blockquote>
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