scholarly journals CCP4i2: the new graphical user interface to theCCP4 program suite

2018 ◽  
Vol 74 (2) ◽  
pp. 68-84 ◽  
Author(s):  
Liz Potterton ◽  
Jon Agirre ◽  
Charles Ballard ◽  
Kevin Cowtan ◽  
Eleanor Dodson ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Structure Determination ◽  
Design Guidelines ◽  
Macromolecular Structure ◽  
Graphical Interface ◽  
Software Suite ◽  
X Ray ◽  
X Ray Crystallography ◽  
Structure Solution

TheCCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introducedCCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition,CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures.

Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMRspectroscopy

1993 ◽  
Vol 26 (1) ◽  
pp. 49-125 ◽  
Author(s):  
Axel T. Brünger ◽  
Michael Nilges
Keyword(s):  
Nmr Spectroscopy ◽  
Structure Determination ◽  
Solution Nmr ◽  
Macromolecular Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Past ◽  
Solution Nmr Spectroscopy

Macromolecular structure determination by X-ray crystallography and solution NMR spectroscopy has experienced unprecedented growth during the past decade.

scholarly journals CCP4 web services

2014 ◽  
Vol 70 (a1) ◽  
pp. C781-C781
Author(s):  
Ville Uski ◽  
Charles Ballard ◽  
Ronan Keegan ◽  
Eugene Krissinel ◽  
Andrey Lebedev ◽  
...  
Keyword(s):  
Web Services ◽  
Solution Process ◽  
Portable Devices ◽  
Molecular Replacement ◽  
Graphical Interface ◽  
X Ray ◽  
X Ray Crystallography ◽  
Structure Solution ◽  
Large Databases ◽  
Linux Cluster

The CCP4 software suite [1] provides a comprehensive set of tools for use in the macromolecule structure solution process by X-ray crystallography. Traditionally, these tools have been run through the graphical interface or the command line on each user's personal workstation. Recently, some of the tools, including the molecular replacement pipelines Balbes [2] and MrBUMP [3] have been provided as web services in the Research Complex at Harwell. These pipelines can be especially useful in cases where there is low sequence identity between the target-structure sequence and that of its set of possible homologues. These services can be accessed through a web client, allowing one to submit molecular replacement jobs to our Linux cluster and view the results from these jobs. The molecular replacement pipelines are ideal candidates for web services, as they require installation and maintenance of large databases and benefit from parallel computing resources, provided by the cluster. Further plans for web services will be discussed. With ever-increasing mobility of scientific setups and the ubiquity of ultra-portable devices, there is a demand for a consistent framework of remote crystallographic computations and data maintenance. This framework is planned to include an interface for synchronising data with the facilities of Diamond Light Source, as well as with local CCP4 GUI-2 setups.

New similarity index for crystal structure determination from X-ray powder diagrams

2005 ◽  
Vol 38 (6) ◽  
pp. 861-866 ◽  
Author(s):  
Detlef Walter Maria Hofmann ◽  
Ludmila Kuleshova
Keyword(s):  
Crystal Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Similarity Index ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
X Ray ◽  
Organic Pigments ◽  
Structure Solution ◽  
Similarity Indices

A new similarity index for automated comparison of powder diagrams is proposed. In contrast to traditionally used similarity indices, the proposed method is valid in cases of large deviations in the cell constants. The refinement according to this index closes the gap between crystal structure prediction and automated crystal structure determination. The opportunities of the new procedure have been demonstrated by crystal structure solution of un-indexed powder diagrams of some organic pigments (PY111, PR181 and Me-PR170).

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