diff --git a/_spotlights/crystfel.md b/_spotlights/crystfel.md new file mode 100644 index 0000000000000000000000000000000000000000..00045877095dbebb6923f40837e79a3846c360aa --- /dev/null +++ b/_spotlights/crystfel.md @@ -0,0 +1,145 @@ +--- +layout: spotlight + +# ----------------------------------------------------------------------------- +# Properties for spotlights list page +# ----------------------------------------------------------------------------- + +# The name of the software +name: CrystFEL in a nutshell +date_added: 2022-08-22 + +# Small preview image shown at the spotlights list page. +# Note: the path is relative to /assets/img/spotlights/ +preview_image: crystfel/crystfel-logo.png + +# One or two sentences describing the software +excerpt: > + CrystFEL is a suite of programs to process + data from "serial crystallography" experiments. + +# ----------------------------------------------------------------------------- +# Properties for individual spotlights page +# ----------------------------------------------------------------------------- +# Entries here will be shown in the green box on the right of the screen. + +# Jumbotron (optional) +# The path is relative to /assets/img/jumbotrons/ +title_image: crystfel-image-1.jpg + +# Title at the top, inside the title-content-container +title: CrystFEL in a nutshell + +# Add at least one keyword +keywords: + - crystallography + - XFEL + - synchrotron + - structural biology + +# The Helmholtz research field +hgf_research_field: Matter + +# At least one responsible centre +hgf_centers: + - Deutsches Elektronen-Synchrotron DESY + +# List of other contributing organisations (optional) +contributing_organisations: + +# List of scientific communities +scientific_community: + - Photon science, X-ray crystallography + +# Impact on community (optional, not implemented yet) +impact_on_community: + +# An e-mail address +contact: thomas.white@desy.de + +# Platforms (optional) +# Provide platforms in this format +# - type: TYPE +# link_as: LINK +# Valid TYPES are: webpage, telegram, mailing-list, twitter, gitlab, github +# Mailing lists should be added as "mailto:mailinglist@url.de" +# More types can be implemented by modifying /_layouts/spotlight.html +platforms: + - type: webpage + link_as: https://desy.de/~twhite/crystfel/ + - type: gitlab + link_as: https://gitlab.desy.de/thomas.white/crystfel/ + - type: github + link_as: https://github.com/taw10/crystfel + +# The software license, please use an SPDX Identifier (https://spdx.org/licenses/) if possible (optional) +license: GPL-3.0-or-later + +# Is the software pricey or free? (optional) +costs: Free + +# What is this software used for in general (e.g. modelling)? (optional, not implemented yet) +software_type: + - + +# The applicaiton type (Desktop, Mobile, Web) (optional, not implemented yet) +application_type: + - Web + +# List of programming languages (optional) +programming_languages: + - C, Python + +# DOI (without URL, just 10.1000/1.0000000 ) (optional) +doi: 10.1107/S0021889812002312 + +# Funding of the software (optional) +funding: + - shortname: DESY + +--- + +# CrystFEL in a nutshell + +[CrystFEL](https://www.desy.de/~twhite/crystfel/) +is a suite of programs to process data from "serial crystallography" experiments. +Datasets from +this type of experiment consist of many thousands of individual diffraction patterns, each one of which +was produced by X-rays scattering from a tiny crystal. This technique is most often used for investigating +the structure of biological molecules such as proteins, but other types of matter have been investigated +as well. The X-rays can come from a synchrotron storage ring such as +[PETRA III](https://photon-science.desy.de/facilities/petra_iii/index_eng.html), or from a free-electron +laser such as the +[European XFEL](https://www.xfel.eu/). +Electron beams in a transmission electron microscope can also be +used. The "serial" mode of data acquisition is particularly relevant for time-resolved experiments - +making so-called "molecular movies". + +To process the data, each diffraction pattern has to be analysed individually. +The first step is to find the +sharp "Bragg" peaks in the pattern, from which the orientation of the crystal as well as the geometrical +parameters of the crystal lattice can be determined. +The intensities of the Bragg peaks then need to be +measured, including very weak peaks whose presence can be inferred from the crystal parameters +despite not being found by the initial peak search. +The intensities from all the patterns are then merged +together to produce a final combined dataset which can be used to determine the structure of the +crystal. + +CrystFEL contains programs to perform each of these steps, brought together with a graphical user +interface. High performance computing is often needed due to the sizes of the datasets, so the GUI can +submit jobs directly via a batch system such as Slurm. +Recently, streaming data interfaces (for example, +based on ZeroMQ) have been implemented, enabling real-time data processing without any +intermediate storage of data. + +The CrystFEL website contains further information including presentation slides, a screencast, citation +lists, API reference and a detailed tutorial. + +<div class="spotlights-text-image"> +<img src="{{ site.directory.images | relative_url}}spotlights/crystfel/Screenshot_crystfel.png" alt="Screenshot of the CrystFEL graphical user interface."> +<span>Screenshot of the CrystFEL graphical user interface being used to examine a serial crystallography +dataset acquired at <a href="https://www.psi.ch/en/swissfel">SwissFEL</a>.</span> +</div> + +See also a <a href="https://www.desy.de/~twhite/crystfel/presentations.html"><i class="fas fa-external-link-alt"></i> presentation video about CrystFEL</a>. diff --git a/assets/img/jumbotrons/crystfel-image-1.jpg b/assets/img/jumbotrons/crystfel-image-1.jpg new file mode 120000 index 0000000000000000000000000000000000000000..d1dfef1850cff416929ec136e4089e65dcf68deb --- /dev/null +++ b/assets/img/jumbotrons/crystfel-image-1.jpg @@ -0,0 +1 @@ +../spotlights/crystfel/crystfel-image-1.JPG \ No newline at end of file diff --git a/assets/img/spotlights/crystfel/Screenshot_crystfel.png b/assets/img/spotlights/crystfel/Screenshot_crystfel.png new file mode 100644 index 0000000000000000000000000000000000000000..214f209948d75a9b5dc766931490180c033de8a7 Binary files /dev/null and b/assets/img/spotlights/crystfel/Screenshot_crystfel.png differ diff --git a/assets/img/spotlights/crystfel/crystfel-image-1.JPG b/assets/img/spotlights/crystfel/crystfel-image-1.JPG new file mode 100644 index 0000000000000000000000000000000000000000..fbb5541d5dfeb9665bd1192e408a599b7cad48e9 Binary files /dev/null and b/assets/img/spotlights/crystfel/crystfel-image-1.JPG differ diff --git a/assets/img/spotlights/crystfel/crystfel-logo.png b/assets/img/spotlights/crystfel/crystfel-logo.png new file mode 100644 index 0000000000000000000000000000000000000000..b8db848df1ca7cbb2e4a58f70373c31c4e641ea6 Binary files /dev/null and b/assets/img/spotlights/crystfel/crystfel-logo.png differ