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Protocols

CCP4mg specifications

Information


Unique identifier OMICS_26711
Name CCP4mg
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Output format GIF,PNG,JPG
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Python
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.10.10
Stability Stable
Source code URL http://www.ccp4.ac.uk/MG/download/ccp4mg-2.10.10-src.tar.gz
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline CCP4mg Team

Additional information


http://www.ccp4.ac.uk/MG/ccp4mg_help2/index.html

Publication for CCP4mg

CCP4mg citations

 (206)
library_books

Conformational dynamics in crystals reveal the molecular bases for D76N beta 2 microglobulin aggregation propensity

2018
Nat Commun
PMCID: 5916882
PMID: 29695721
DOI: 10.1038/s41467-018-04078-y

[…] cement using the program PHASER and wt β2m as search model (pdb ID 2YXF). All the structures were refined with Phenix refine and manual model building and structure analysis were performed with COOT. CCP4MG was used for the preparation of the figures. […]

library_books

Bacteroides thetaiotaomicron generates diverse α mannosidase activities through subtle evolution of a distal substrate binding motif

2018
Acta Crystallogr D Struct Biol
PMCID: 5930347
PMID: 29717710
DOI: 10.1107/S2059798318002942

[…] factors and final atomic models have been deposited in the PDB with accession codes 6f8z (BT3130), 6f90 (BT3130–ManI), 6f91 (BT3965) and 6f92 (BT3965–ManI). All structural figures were prepared using CCP4mg (McNicholas et al., 2011). […]

call_split

CCP4i2: the new graphical user interface to the CCP4 program suite

2018
Acta Crystallogr D Struct Biol
PMCID: 5947771
PMID: 29533233
DOI: 10.1107/S2059798317016035
call_split See protocol

[…] s from processing data to validation and analysis of the final structure. Although most tasks are running nongraphical programs, there are certain tasks that run interactive software such as Coot and CCP4mg. The integration of these programs into the CCP4i2 framework makes their use less error-prone, simplifies movement of data between applications, and creates a permanent record of the data and f […]

library_books

Distributed computing for macromolecular crystallography

2018
Acta Crystallogr D Struct Biol
PMCID: 5947778
PMID: 29533240
DOI: 10.1107/S2059798317014565

[…] out quotas for disk storage and CPU time. In contrast to web applications, interactivity is not an assumed property of web services, although certain interactive elements, such as molecular graphics (CCP4mg; McNicholas et al., 2011), can be used as part of the report system. In the most straightforward implementation, a web service is expected to provide a user with facilities to upload data, star […]

library_books

Human ex vivo prostate tissue model system identifies ING3 as an oncoprotein

2018
Br J Cancer
PMCID: 5846061
PMID: 29381681
DOI: 10.1038/bjc.2017.447

[…] t form an H3K4me3-binding aromatic cage in other ING proteins (; ). Thus we predicted the structure of ING3PHD using Phyre2 () and superimposed it with the structure of ING4PHD-bound to H3K4me3 using CCP4mg () (). The overlay of ING3PHD and ING4PHD suggests that Y362, S369, and W385 of ING3 would indeed form an aromatic cage similar to ING4 and thus mediate interactions with H3K4me3. To confirm th […]

call_split

Structural and functional characterization of shaft, anchor, and tip proteins of the Mfa1 fimbria from the periodontal pathogen Porphyromonas gingivalis

2018
Sci Rep
PMCID: 5789003
PMID: 29379120
DOI: 10.1038/s41598-018-20067-z
call_split See protocol

[…] sidues were in the Ramachandran favored or allowed regions for the mMfa1, pMfa1Δ9, Mfa2 and pMfa3 structures respectively. Crystallographic statistics are presented in Table . Figures were drawn with CCP4MG. The X-ray coordinates and structure factors have been deposited in the Protein Data Bank under accession codes 5nf2, 5nf3, 5nf1 and 5nf4. […]

Citations

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CCP4mg institution(s)
York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK; Department of Biochemistry, University of Oxford, Oxford, UK
CCP4mg funding source(s)
Supported by the Science and Technology Facilities Council through CCP4.

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