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Hi Tim,<br>
<br>
thanks for bringing this! Frankly I was not aware of SQUEEZE method
likely because I'm not a heavy user of Platon. Anyways, this
conversation prompted me to do some reading this morning:<br>
<br>
<a class="moz-txt-link-freetext" href="http://journals.iucr.org/a/issues/1990/03/00/ge0049/ge0049.pdf">http://journals.iucr.org/a/issues/1990/03/00/ge0049/ge0049.pdf</a><br>
<a class="moz-txt-link-freetext" href="http://scripts.iucr.org/cgi-bin/paper?S2053229614024929">http://scripts.iucr.org/cgi-bin/paper?S2053229614024929</a><br>
<a class="moz-txt-link-freetext" href="http://web.mit.edu/platon_v40505/platon/docs/platon/aca98.html">http://web.mit.edu/platon_v40505/platon/docs/platon/aca98.html</a><br>
<br>
Here is what I gather from this. Well, first we are talking about
small-molecule crystallography here, with all the implications. It
may happen that crystals contain areas occupied by disordered
solvent that is impractical to account for in terms of atomic model.
I'm not an expert in small molecule crystallography but it sounds to
me like this is something that rather does not happen all that often
compared to bio-crystallography where the disordered (bulk) solvent
typically occupies from 10 to 90% of the unit cell volume. Now,
given high accuracy standards in small molecule crystallography this
inability to account for disordered scattering poses a big problem
as it hampers refinement and potentially highly accurate map
interpretation. The SQUEEZE method provides a way to identify such
regions of disordered scatterers and accounting for their
contribution to the total model structure factors. For example,
citing <br>
<br>
A. L. Spek<br>
Acta Cryst. (2015). C71, 9-18<br>
�PLATON SQUEEZE: a tool for the calculation of the disordered
solvent contribution to the calculated structure factors<br>
<br>
"""<br>
The completion of a crystal structure determination is often
hampered by the presence of embedded solvent molecules or ions that
are seriously disordered. Their contribution to the calculated
structure factors in the least-squares refinement of a crystal
structure has to be included in some way. Traditionally, an
atomistic solvent disorder model is attempted. Such an approach is
generally to be preferred, but it does not always lead to a
satisfactory result and may even be impossible in cases where
channels in the structure are filled with continuous electron
density. This paper documents the SQUEEZE method as an alternative
means of addressing the solvent disorder issue. It conveniently
interfaces with the 2014 version of the least-squares refinement
program SHELXL [Sheldrick (2015). Acta Cryst. C71. In the press] and
other refinement programs that accept externally provided fixed
contributions to the calculated structure factors. The PLATON
SQUEEZE tool calculates the solvent contribution to the structure
factors by back-Fourier transformation of the electron density found
in the solvent-accessible region of a phase-optimized difference
electron-density map. The actual least-squares structure refinement
is delegated to, for example, SHELXL.<br>
"""<br>
<br>
Here is what we are dealing with in our case. Macro-molecular
crystals on average contain ~50% of the disordered (bulk) solvent.
Most (if not all) software packages automatically account for this
disordered solvent by defining the total model structure factors as<br>
<br>
Fmodel = k_total * (Fcalc_atoms + Fbulk) .<br>
<br>
Fmodel is then used in all calculations such as R-factors,
refinement targets, various maps, etc. Up to this point, it is along
the lines of what SQUEEZE does, indeed.<br>
<br>
Different bulk-solvent models can be used to calculate Fbulk
contribution. Two major models are in use: Babinet-based model (used
in SHELX) and Flat model (used in CNS, REFMAC, PHENIX).<br>
<br>
Both models have their pros and cons. For example, the downside of
Babinet-based model is that it holds true for resolutions lower than
10-15A:<br>
<br>
<meta charset="utf-8">
Podjarny, A. D. & Urzhumtsev, A. G. (1997). <br>
<a class="moz-txt-link-freetext" href="http://www.ccp4.ac.uk/newsletters/newsletter38/08_solvent.html">http://www.ccp4.ac.uk/newsletters/newsletter38/08_solvent.html</a><br>
<br>
and is handicapped at resolutions between 10-15 and 5-6A (where
disordered solvent contribution vanishes). The good thing about it
is that it does not implies masking bias.<br>
<br>
Unlike Babinet model, Flat bulk-solvent model accounts for
disordered solvent pretty well across all resolution ranges. The
downside of the flat bulk solvent model is what we are trying to
address using Polder maps. <br>
<br>
So.. The way flat bulk solvent model works is it defines a solvent
mask which is a binary function with 0 inside macro-molecule and 1
outside (Jiang&Brunger, 1997). Then this function is Fourier
transformed into structure factors Fmask and that are then added to
the total model structure factors with some refinable scale k_mask:<br>
<br>
Fmodel = k_total * (Fcalc_atoms + k_mask * Fmask) .<br>
<br>
The problem with this approach is that the solvent is "poured"
everywhere in the unit cell where there is no atomic model. For
example, if there is a ligand that is not placed yet or a loop that
is not modeled yet, the flat bulk solvent will fill the gap. Most of
the time this will not pose much trouble as atomic features
typically stand above the noise or/and solvent density. However, in
cases when feature that one tries to model is weak (mobile,
partially occupied ligand or flexible disordered loop) the flat
solvent model may obscure it by flattening corresponding density in
the region of interest. This is the issue that Polder residual OMIT
map is meant to address by excluding bulk-solvent contribution from
specifically defined regions and therefore provide mask bias free
view of residual map in that region. I think this is not quite the
same as what SQUEEZE method does.<br>
<br>
In fact Polded OMIT map is a single iteration of a more general
procedure described in Section 2.4 and Figure 6 here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://journals.iucr.org/d/issues/2015/03/00/lv5075/lv5075.pdf">http://journals.iucr.org/d/issues/2015/03/00/lv5075/lv5075.pdf</a><br>
<br>
All the best,<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 4/21/16 06:21, Tim Gruene wrote:<br>
</div>
<blockquote cite="mid:4786506.QFeOrCPCTp@hilbert" type="cite">
<pre wrap="">Dear Dorothee,
With squeeze, you remove solvent in order to make features visible lying
underneath the noise density of the solvent. That's reminiscent to me as the
cartoon on p.9 of the phenix_polder.pdf
In Platon, the structure factors are calculated from the density in the
solvent region, Eq. (4) in the Platon paper. That appears to be the same as
explained for phenix_polder on p. 4, except that phenix replaces
rho(x_solvent) with 1 for the mask. The equation on p.2 of the PDF-file is
identical to the line below Eq. 4 in the SQUEEZE paper, so it seems
conceptually pretty much the same to me.
Since SQUEEZE was presented at the ACA in 1998 (based on a paper from 1990), I
thought you may have been motivated by it. It is probably not much surprising
that good ideas get invented at various places.
Best wishes,
Tim
On Wednesday, April 20, 2016 01:59:34 PM you wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Tim,
I quickly looked over the SQUEEZE command in PLATON (are you referring to:
<a class="moz-txt-link-freetext" href="http://scripts.iucr.org/cgi-bin/paper?S2053229614024929">http://scripts.iucr.org/cgi-bin/paper?S2053229614024929</a> ?). To me, it does
not seem to be related to phenix.polder.
There is no complicated math involved in polder; slides 2-4 are a summary
of the flat bulk-solvent model (which is used in Phenix, and which is also
available in CNS and REFMAC).
The flat bulk-solvent model is described first here:
Phillips, S. E. (1980). *J. Mol. Biol.* *142*, 531�554.
I uses a similar concept than SQUEEZE, i.e. the total structure factor is
expressed as a sum of contributions from protein model and disordered
solvent.
More references can be found in this review about bulk solvent models in MX:
Weichenberger, C. X., Afonine, P. V, Kantardjieff, K. & Rupp, B. (2015).
*Acta Crystallogr. Sect. D Biol. Crystallogr.* *71*, 1023�1038.
The polder tool uses the bulk solvent mask (as it is generated for other
functionalities in phenix, such as phenix.refine), and then modifies the
mask locally. I am sorry if the presentation file is misleading, I should
maybe add some references to make clear what is summary and what is related
to the polder tool.
Best wishes,
Dorothee
PS:
I did not understand how the name "squeeze" relates to "polder"...
On Wed, Apr 20, 2016 at 12:07 PM, Tim Gruene <a class="moz-txt-link-rfc2396E" href="mailto:tim.gruene@psi.ch"><tim.gruene@psi.ch></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hi Pavel,
this is an interesting concept. It seems related to the SQUEEZE command in
platon - even the name appears to suggest a relationship. I did not
understand
the maths entirely: Are they similar concept, or do I misinterprete?
Best,
Tim
On Wednesday, April 20, 2016 07:28:16 AM Pavel Afonine wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello,
it's good to know it was useful for you, thanks for feedback! I afraid
it's too new so that we don't have a publication to cite yet. We are
working on a manuscript but it may take a little while before it appears
somewhere. For now I guess you can use this link (unless Dorothee has a
better idea)
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/phenix_polder.pdf">http://www.phenix-online.org/presentations/phenix_polder.pdf</a>
and use official Phenix citation:
Acta Cryst. D66, 213-221 (2010).
That's all we have at the moment anyway.
All the best,
Pavel
On 4/20/16 04:18, Lund Bjarte Aarmo wrote:
</pre>
<blockquote type="cite">
<pre wrap="">DearDorothee and phenixbb,
I found this software very useful for protein-fragment complexes with
weak electron density. I was wondering how the software should be
</pre>
</blockquote>
</blockquote>
<pre wrap="">
cited?
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Kind regards,
Bjarte Aarmo Lund
PhD candidate
UiT � The arctic university of Norway
*From:*phenixbb-bounces@phenix-online.org
[<a class="moz-txt-link-freetext" href="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</a>] *On Behalf Of *Dorothee
Liebschner
*Sent:* 22. mars 2016 21:46
*To:* PHENIX user mailing list <a class="moz-txt-link-rfc2396E" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a>
*Subject:* [phenixbb] phenix.polder - tool for calculating omit maps
by excluding bulk solvent
Dear phenix users,
Starting from the nightly build dev-2356, a new tool for calculating
ligand omit-maps, called 'polder', is included in phenix.
Usage:
phenix.polder model.pdb data.mtz selection='chain A and resseq
</pre>
</blockquote>
</blockquote>
<pre wrap="">
123�
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Phenix.polder calculates omit maps for atom selections by preventing
the bulk solvent mask to flood into the atom selection area and its
vicinity. The tool can be useful in cases where the density of the
selected atoms is weak and possibly obscured by bulk solvent.
Polder produces less biased maps compared to procedures where the atom
selection occupancy is set to zero, and the atoms are included in the
solvent mask calculation (in that case, the resulting difference
density can have similar shape than the selected atoms). Phenix.polder
excludes a larger volume from the bulk solvent and therefore prevents
misinterpreting bulk solvent density as omit density.
If you want to know more about how the tool is working and to see some
examples, have a look at the presentation file:
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/presentations/phenix_polder.pdf">https://www.phenix-online.org/presentations/phenix_polder.pdf</a>.
The documentation page can be found here:
<a class="moz-txt-link-abbreviated" href="http://www.phenix-online.org/version_docs/dev-2356/reference/polder.html">www.phenix-online.org/version_docs/dev-2356/reference/polder.html</a>
Best wishes,
Dorothee
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<pre wrap="">
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Tim Gruene
- - persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
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