-----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:

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)

http://www.phenix-online.org/presentations/phenix_polder.pdf

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:

...

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 cited?

Kind regards,

Bjarte Aarmo Lund

PhD candidate

UiT – The arctic university of Norway

*From:*[email protected] [mailto:[email protected]] *On Behalf Of *Dorothee Liebschner *Sent:* 22. mars 2016 21:46 *To:* PHENIX user mailing list *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 123’

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: https://www.phenix-online.org/presentations/phenix_polder.pdf.

The documentation page can be found here:

www.phenix-online.org/version_docs/dev-2356/reference/polder.html

Best wishes,

Dorothee

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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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:
> Hi Tim,
> 
> I quickly looked over the SQUEEZE command in PLATON (are you referring to:
> http://scripts.iucr.org/cgi-bin/paper?S2053229614024929 ?). 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  wrote:
> > -----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:
> > > 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)
> > > 
> > > http://www.phenix-online.org/presentations/phenix_polder.pdf
> > > 
> > > 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:
> > > > 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
> > 
> > cited?
> > 
> > > > Kind regards,
> > > > 
> > > > Bjarte Aarmo Lund
> > > > 
> > > > PhD candidate
> > > > 
> > > > UiT – The arctic university of Norway
> > > > 
> > > > *From:*[email protected]
> > > > [mailto:[email protected]] *On Behalf Of *Dorothee
> > > > Liebschner
> > > > *Sent:* 22. mars 2016 21:46
> > > > *To:* PHENIX user mailing list 
> > > > *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
> > 
> > 123’
> > 
> > > > 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:
> > > > https://www.phenix-online.org/presentations/phenix_polder.pdf.
> > > > 
> > > > The documentation page can be found here:
> > > > 
> > > > www.phenix-online.org/version_docs/dev-2356/reference/polder.html
> > > > 
> > > > Best wishes,
> > > > 
> > > > Dorothee
> > > > 
> > > > 
> > > > 
> > > > _______________________________________________
> > > > phenixbb mailing list
> > > > [email protected]
> > > > http://phenix-online.org/mailman/listinfo/phenixbb
> > > > Unsubscribe: [email protected]
> > 
> > - --
> > - --
> > Paul Scherrer Institut
> > Tim Gruene
> > - - persoenlich -
> > OFLC/102
> > CH-5232 Villigen PSI
> > phone: +41 (0)56 310 5297
> > 
> > GPG Key ID = A46BEE1A
> > -----BEGIN PGP SIGNATURE-----
> > Version: GnuPG v2
> > 
> > iD8DBQFXF9NpUxlJ7aRr7hoRApIFAKCZ6gKgFMeeU4DSZfr5i/5Z3inC/ACeOmIh
> > sjQCpCYG2CkH/N/RoIfhApQ=
> > =t+dS
> > -----END PGP SIGNATURE-----
> > 
> > 
> > _______________________________________________
> > phenixbb mailing list
> > [email protected]
> > http://phenix-online.org/mailman/listinfo/phenixbb
> > Unsubscribe: [email protected]
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Pavel, thank you, this is a very interesting and clear explanation! Best wishes, Tim On Thursday, April 21, 2016 08:57:20 AM Pavel Afonine wrote:

Hi Tim,

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:

http://journals.iucr.org/a/issues/1990/03/00/ge0049/ge0049.pdf http://scripts.iucr.org/cgi-bin/paper?S2053229614024929 http://web.mit.edu/platon_v40505/platon/docs/platon/aca98.html

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

A. L. Spek Acta Cryst. (2015). C71, 9-18 PLATON SQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors

""" 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. """

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

Fmodel = k_total * (Fcalc_atoms + Fbulk) .

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.

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).

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:

Podjarny, A. D. & Urzhumtsev, A. G. (1997). http://www.ccp4.ac.uk/newsletters/newsletter38/08_solvent.html

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.

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.

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:

Fmodel = k_total * (Fcalc_atoms + k_mask * Fmask) .

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.

In fact Polded OMIT map is a single iteration of a more general procedure described in Section 2.4 and Figure 6 here:

http://journals.iucr.org/d/issues/2015/03/00/lv5075/lv5075.pdf

All the best, Pavel

On 4/21/16 06:21, Tim Gruene wrote:

...

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:

...

Hi Tim,

I quickly looked over the SQUEEZE command in PLATON (are you referring to: http://scripts.iucr.org/cgi-bin/paper?S2053229614024929 ?). 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 wrote:

...

-----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:

...

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)

http://www.phenix-online.org/presentations/phenix_polder.pdf

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:

...

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

cited?

...

...

Kind regards,

Bjarte Aarmo Lund

PhD candidate

UiT – The arctic university of Norway

*From:*[email protected] [mailto:[email protected]] *On Behalf Of *Dorothee Liebschner *Sent:* 22. mars 2016 21:46 *To:* PHENIX user mailing list *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

123’

...

...

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: https://www.phenix-online.org/presentations/phenix_polder.pdf.

The documentation page can be found here:

www.phenix-online.org/version_docs/dev-2356/reference/polder.html

Best wishes,

Dorothee

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

- -- - -- Paul Scherrer Institut Tim Gruene - - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297

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