dr. Eugene Krissinel

Science and Technology Facilities Council,
CCP4 core group
Oxford, UK

HT3: Processing & Structure determination

L1 : Structure Solution in CCP4 Cloud

CCP4 Cloud is a front-end for the CCP4 Software Suite, which represents a conceptually new approach to organising and maintaining crystallographic projects in CCP4 and running CCP4 tasks. Unlike conventional type of front-end, which usually keeps projects and runs tasks on the user’s machine, CCP4 Cloud exploits the paradigm of remote computing, when all projects and data are kept online and tasks are executed on remote servers, “in cloud”.  CCP4 Cloud is accessible through any web browser, making it easy to use and accessible from anywhere with internet connection. CCP4 maintains a public instance of CCP4 Cloud at RAL Harwell (https://cloud.ccp4.ac.uk). If necessary, CCP4 Cloud servers may be placed on the user’s machine, in which case all data and projects are kept locally and CCP4 Cloud behaves as a desktop GUI (so-called “desktop mode”). Starting from CCP4 series 7.1, CCP4 Cloud is included in the distributed package and can be started out-of-the-box by clicking on icon launchers.

A few important CCP4 components: data processing software, Coot, CCP4 Molecular Graphics and some others, can be used only on users’ machines. They are linked with CCP4 Cloud automatically once CCP4 is installed on the user’s computer.

CCP4 Cloud’s key benefits include high platform compatibility, access to significant computational resources and suitability for team work. CCP4 Cloud projects are accessible from any geographic location and computing platform; with Cloud, one can solve structures even from tablet devices and mobile phones. A number of internet resources are seamlessly integrated; structures from PDB, UniProt, AlphaFold and ESM databases can be imported instantly, 3rd party software such as PDB-REDO and Buster from Global Phasing are made available as well. Time-consuming tasks, such as structure auto-solvers and auto-builders, can be conducted in shorter time without the need for specialised hardware installed locally.

CCP4 Cloud projects can be exported as single files and reimported back in Cloud as necessary. When several researchers need to work on a project simultaneously, it can be shared between them online, regardless of their location, allowing for efficient communication and collaboration in real-time.

Retaining structure-solution projects is as important as retaining experimental data. This can be useful for the subsequent understanding of ambiguous structural features, revisiting and revising structural studies, education, facilitating the peer-review publication process, training and software development. Starting from 1st January 2023, CCP4 Cloud projects can be archived and referenced in publications or similar reports by a unique Archive ID. Archived projects represent a missing link between experimental data and the final structure, deposited in the wwPDB. This is a new initiative on keeping information complementary to PDB depositions and facilitating the exchange of knowledge and structure solution practices in the structural biology community.

The lecture will give a practical introduction in CCP4 Cloud:

  • principles of CCP4 Cloud interface
  • project types and their initiation
  • principles of project development
  • importing data and exporting results
  • forming and running crystallographic tasks
  • use of documentation resources and tutorials for self-education
  • overview of typical projects for molecular replacement and experimental phasing
  • automation facilities
  • overview of available crystallographic tasks
  • project export/import and sharing
  • and more