Spotlights desy crystfel

_spotlights/crystfel.md

+---
+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>.

assets/img/jumbotrons/crystfel-image-1.jpg

+../spotlights/crystfel/crystfel-image-1.JPG
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