htdocs update (master)

_sources/about.rst.txt

@@ -2,6 +2,22 @@
 About
 +++++
 
+Atomic structures are vital for scientific research.  From understanding
+the mechanisms of biology to the design of new materials for industrial applications,
+knowing the placement of atoms in a molecule assists in the control of disease progression,
+drug design, the development of therapies such as vaccines, building new compounds
+for better batteries, and finding new methods of carbon sequestration.
+
+Crystallography is one of the prime technologies used to generate high quality structures,
+generated from crystallographic data collected at large facilities like synchrotrons and
+X-ray free electron lasers, on large micro electron diffraction instruments, at neutron
+sources, or at home in a lab.  At these facilities and instruments, crystals are either
+rotated in a beam of photons, neutrons, or electrons, or are exposed one at a time in a
+serial experiment, and diffraction data from detectors are collected and stored in image
+files. The DIALS software package (Diffraction Integration for Advanced Light Sources) is
+used throughout the world for processing crystallographic data in automated pipelines or
+through graphical user interfaces.
+
 The DIALS software is developed in a fully open-source, collaborative
 environment. The main development teams are based at `Diamond Light Source`_
 and `CCP4`_, in the UK, and at `Lawrence Berkeley National Laboratory`_, USA.

_sources/index.rst.txt

@@ -42,6 +42,17 @@ For feature requests, bug reports or any other information, please contact
 the DIALS developers at [email protected], or post an
 `issue`_.
 
+Citing DIALS
+============
+
+Researchers using DIALS to process their data should cite the DIALS publication:
+
+**DIALS: implementation and evaluation of a new integration package**.
+Winter G, Waterman DG, Parkhurst JM, Brewster AS, Gildea RJ, Gerstel M, Fuentes-Montero L, Vollmar M, Michels-Clark T, Young ID, Sauter NK, Evans G (2018).
+Acta Crystallogr D Struct Biol 74, 85-97
+
+To acknowledge direct support from the :ref:`DIALS Resource<national_resource>`, such as when Resource staff assist with data collection or processing, or to acknowledge DIALS software integration at a facility or instrument, please acknowledge NiH grant R24GM154040.
+
 Funding
 =======
 

_sources/publications.rst.txt

@@ -10,6 +10,7 @@ DIALS Journal Articles
 * .. pubmed:: 35647922 xia2.multiplex
 * .. pubmed:: 34747533 DIALS as a toolkit
 * .. pubmed:: 32254063 dials.scale
+* .. pubmed:: 31692470 XFEL error modeling
 * .. pubmed:: 30950396 How best to use photons
 * .. pubmed:: 30198898 Serial crystallography
 * .. pubmed:: 29872002 Electron diffraction
@@ -29,7 +30,14 @@ DIALS Journal Articles
 DIALS Application to XFEL Crystallography
 -----------------------------------------
 
+* .. pubmed:: 37797025 ribonucleotide reductase R2 protein radical
+* .. pubmed:: 37138085 PSII O2 formation
 * .. pubmed:: 35046599 Chemical Crystallography at XFELs
+* .. pubmed:: 30405241 PSII Kok cycle
+* .. pubmed:: 28835537 M2 proton channel
+* .. pubmed:: 27871088 PSII RT
+* .. pubmed:: 27680699 De novo phasing
+* .. pubmed:: 26422513 Multitemperature dynamics
 * .. pubmed:: 26352473 synuclein
 * .. pubmed:: 26280336 synaptotagmin-SNARE
 * .. pubmed:: 26057680 Ginn 2015b

about.html

@@ -47,6 +47,20 @@
 
   <section id="about">
 <h1>About<a class="headerlink" href="#about" title="Link to this heading">¶</a></h1>
+<p>Atomic structures are vital for scientific research.  From understanding
+the mechanisms of biology to the design of new materials for industrial applications,
+knowing the placement of atoms in a molecule assists in the control of disease progression,
+drug design, the development of therapies such as vaccines, building new compounds
+for better batteries, and finding new methods of carbon sequestration.</p>
+<p>Crystallography is one of the prime technologies used to generate high quality structures,
+generated from crystallographic data collected at large facilities like synchrotrons and
+X-ray free electron lasers, on large micro electron diffraction instruments, at neutron
+sources, or at home in a lab.  At these facilities and instruments, crystals are either
+rotated in a beam of photons, neutrons, or electrons, or are exposed one at a time in a
+serial experiment, and diffraction data from detectors are collected and stored in image
+files. The DIALS software package (Diffraction Integration for Advanced Light Sources) is
+used throughout the world for processing crystallographic data in automated pipelines or
+through graphical user interfaces.</p>
 <p>The DIALS software is developed in a fully open-source, collaborative
 environment. The main development teams are based at <a class="reference external" href="http://www.diamond.ac.uk/Home.html">Diamond Light Source</a>
 and <a class="reference external" href="http://www.ccp4.ac.uk/">CCP4</a>, in the UK, and at <a class="reference external" href="http://www.lbl.gov/">Lawrence Berkeley National Laboratory</a>, USA.

index.html

@@ -67,6 +67,14 @@ <h2>Contact<a class="headerlink" href="#contact" title="Link to this heading">¶
 the DIALS developers at <a class="reference external" href="mailto:dials-support&#37;&#52;&#48;lists&#46;sourceforge&#46;net">dials-support<span>&#64;</span>lists<span>&#46;</span>sourceforge<span>&#46;</span>net</a>, or post an
 <a class="reference external" href="https://github.com/dials/dials/issues">issue</a>.</p>
 </section>
+<section id="citing-dials">
+<h2>Citing DIALS<a class="headerlink" href="#citing-dials" title="Link to this heading">¶</a></h2>
+<p>Researchers using DIALS to process their data should cite the DIALS publication:</p>
+<p><strong>DIALS: implementation and evaluation of a new integration package</strong>.
+Winter G, Waterman DG, Parkhurst JM, Brewster AS, Gildea RJ, Gerstel M, Fuentes-Montero L, Vollmar M, Michels-Clark T, Young ID, Sauter NK, Evans G (2018).
+Acta Crystallogr D Struct Biol 74, 85-97</p>
+<p>To acknowledge direct support from the <a class="reference internal" href="national_resource.html#national-resource"><span class="std std-ref">DIALS Resource</span></a>, such as when Resource staff assist with data collection or processing, or to acknowledge DIALS software integration at a facility or instrument, please acknowledge NiH grant R24GM154040.</p>
+</section>
 <section id="funding">
 <h2>Funding<a class="headerlink" href="#funding" title="Link to this heading">¶</a></h2>
 <p>DIALS development at <a class="reference external" href="http://www.diamond.ac.uk/">Diamond Light Source</a> is performed by employees of

publications.html

@@ -75,6 +75,12 @@ <h2>DIALS Journal Articles<a class="headerlink" href="#dials-journal-articles" t
 </div>
 </li>
 <li><div class="line-block">
+<div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798319012877" target="_blank">SAD phasing of XFEL data depends critically on the error model</a></div>
+<div class="line">Brewster AS, Bhowmick A, Bolotovsky R, Mendez D, Zwart PH, Sauter NK.</div>
+<div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>75</strong>, 959-968 (01 Nov 2019). [PMID:31692470] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC6834081/" target="_blank">PMC6834081</a>]</div>
+</div>
+</li>
+<li><div class="line-block">
 <div class="line"><a class="reference external" href="https://doi.org/10.1107/S2059798319003528" target="_blank">How best to use photons</a></div>
 <div class="line">Winter G, Gildea RJ, Paterson NG, Beale J, Gerstel M, Axford D, Vollmar M, McAuley KE, Owen RL, Flaig R, Ashton AW, Hall DR.</div>
 <div class="line"><em>Acta Crystallogr D Struct Biol</em> <strong>75</strong>, 242-261 (01 Mar 2019). [PMID:30950396] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC6450062/" target="_blank">PMC6450062</a>]</div>
@@ -159,12 +165,54 @@ <h2>DIALS Journal Articles<a class="headerlink" href="#dials-journal-articles" t
 <h2>DIALS Application to XFEL Crystallography<a class="headerlink" href="#dials-application-to-xfel-crystallography" title="Link to this heading">¶</a></h2>
 <ul>
 <li><div class="line-block">
+<div class="line"><a class="reference external" href="https://doi.org/10.1126/science.adh8160" target="_blank">Structure of a ribonucleotide reductase R2 protein radical</a></div>
+<div class="line">Lebrette H, Srinivas V, John J, Aurelius O, Kumar R, Lundin D, Brewster AS, Bhowmick A, Sirohiwal A, Kim IS, Gul S, Pham C, Sutherlin KD, Simon P, Butryn A, Aller P, Orville AM, Fuller FD, Alonso-Mori R, Batyuk A, Sauter NK, Yachandra VK, Yano J, Kaila VRI, Sjöberg BM, Kern J, Roos K, Högbom M.</div>
+<div class="line"><em>Science</em> <strong>382</strong>, 109-113 (06 Oct 2023). [PMID:37797025] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC7615503/" target="_blank">PMC7615503</a>]</div>
+</div>
+</li>
+<li><div class="line-block">
+<div class="line"><a class="reference external" href="https://doi.org/10.1038/s41586-023-06038-z" target="_blank">Structural evidence for intermediates during O<sub>2</sub> formation in photosystem II</a></div>
+<div class="line">Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK.</div>
+<div class="line"><em>Nature</em> <strong>617</strong>, 629-636 (1 May 2023). [PMID:37138085] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC10191843/" target="_blank">PMC10191843</a>]</div>
+</div>
+</li>
+<li><div class="line-block">
 <div class="line"><a class="reference external" href="https://doi.org/10.1038/s41586-021-04218-3" target="_blank">Chemical crystallography by serial femtosecond X-ray diffraction</a></div>
 <div class="line">Schriber EA, Paley DW, Bolotovsky R, Rosenberg DJ, Sierra RG, Aquila A, Mendez D, Poitevin F, Blaschke JP, Bhowmick A, Kelly RP, Hunter M, Hayes B, Popple DC, Yeung M, Pareja-Rivera C, Lisova S, Tono K, Sugahara M, Owada S, Kuykendall T, Yao K, Schuck PJ, Solis-Ibarra D, Sauter NK, Brewster AS, Hohman JN.</div>
 <div class="line"><em>Nature</em> <strong>601</strong>, 360-365 (1 Jan 2022). [PMID:35046599] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC8770144/" target="_blank">PMC8770144</a>]</div>
 </div>
 </li>
 <li><div class="line-block">
+<div class="line"><a class="reference external" href="https://doi.org/10.1038/s41586-018-0681-2" target="_blank">Structures of the intermediates of Kok's photosynthetic water oxidation clock</a></div>
+<div class="line">Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK.</div>
+<div class="line"><em>Nature</em> <strong>563</strong>, 421-425 (1 Nov 2018). [PMID:30405241] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC6485242/" target="_blank">PMC6485242</a>]</div>
+</div>
+</li>
+<li><div class="line-block">
+<div class="line"><a class="reference external" href="https://doi.org/10.1073/pnas.1705624114" target="_blank">XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction</a></div>
+<div class="line">Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF.</div>
+<div class="line"><em>Proc Natl Acad Sci U S A</em> <strong>114</strong>, 13357-13362 (19 Dec 2017). [PMID:28835537] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC5754760/" target="_blank">PMC5754760</a>]</div>
+</div>
+</li>
+<li><div class="line-block">
+<div class="line"><a class="reference external" href="https://doi.org/10.1038/nature20161" target="_blank">Structure of photosystem II and substrate binding at room temperature</a></div>
+<div class="line">Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J.</div>
+<div class="line"><em>Nature</em> <strong>540</strong>, 453-457 (15 Dec 2016). [PMID:27871088] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC5201176/" target="_blank">PMC5201176</a>]</div>
+</div>
+</li>
+<li><div class="line-block">
+<div class="line"><a class="reference external" href="https://doi.org/10.1038/nature19825" target="_blank">De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure</a></div>
+<div class="line">Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS.</div>
+<div class="line"><em>Nature</em> <strong>539</strong>, 43-47 (03 Nov 2016). [PMID:27680699] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC5161637/" target="_blank">PMC5161637</a>]</div>
+</div>
+</li>
+<li><div class="line-block">
+<div class="line"><a class="reference external" href="https://doi.org/10.7554/eLife.07574" target="_blank">Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography</a></div>
+<div class="line">Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS.</div>
+<div class="line"><em>Elife</em> <strong>4</strong> (30 Sep 2015). [PMID:26422513] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4721965/" target="_blank">PMC4721965</a>]</div>
+</div>
+</li>
+<li><div class="line-block">
 <div class="line"><a class="reference external" href="https://doi.org/10.1038/nature15368" target="_blank">Structure of the toxic core of α-synuclein from invisible crystals</a></div>
 <div class="line">Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, Eisenberg DS.</div>
 <div class="line"><em>Nature</em> <strong>525</strong>, 486-90 (24 Sep 2015). [PMID:26352473] [PMC reprint: <a class="reference external" href="http://ncbi.nlm.nih.gov/pmc/articles/PMC4791177/" target="_blank">PMC4791177</a>]</div>