PMID- 21460457
OWN - NLM
STAT- MEDLINE
DA  - 20110404
DCOM- 20110627
LR  - 20140820
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 67
IP  - Pt 4
DP  - 2011 Apr
TI  - Presenting your structures: the CCP4mg molecular-graphics software.
PG  - 386-94
LID - 10.1107/S0907444911007281 [doi]
AB  - CCP4mg is a molecular-graphics program that is designed to give rapid access to
      both straightforward and complex static and dynamic representations of
      macromolecular structures. It has recently been updated with a new interface that
      provides more sophisticated atom-selection options and a wizard to facilitate the
      generation of complex scenes. These scenes may contain a mixture of
      coordinate-derived and abstract graphical objects, including text objects,
      arbitrary vectors, geometric objects and imported images, which can enhance a
      picture and eliminate the need for subsequent editing. Scene descriptions can be 
      saved to file and transferred to other molecules. Here, the substantially
      enhanced version 2 of the program, with a new underlying GUI toolkit, is
      described. A built-in rendering module produces publication-quality images.
FAU - McNicholas, S
AU  - McNicholas S
AD  - York Structural Biology Laboratory, Department of Chemistry, University of York, 
      Heslington, York, England. mcnicholas@ysbl.york.ac.uk
FAU - Potterton, E
AU  - Potterton E
FAU - Wilson, K S
AU  - Wilson KS
FAU - Noble, M E M
AU  - Noble ME
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20110318
PL  - England
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Proteins)
SB  - IM
MH  - Amino Acid Sequence
MH  - Computer Graphics
MH  - Crystallography, X-Ray/*methods
MH  - Databases, Protein
MH  - Models, Molecular
MH  - Molecular Sequence Data
MH  - Protein Structure, Quaternary
MH  - Protein Structure, Tertiary
MH  - Proteins/*analysis
MH  - Sequence Alignment
MH  - *Software Design
MH  - Surface Properties
PMC - PMC3069754
OID - NLM: PMC3069754
EDAT- 2011/04/05 06:00
MHDA- 2011/06/28 06:00
CRDT- 2011/04/05 06:00
PHST- 2010/10/04 [received]
PHST- 2011/02/25 [accepted]
PHST- 2011/03/18 [epublish]
AID - S0907444911007281 [pii]
AID - 10.1107/S0907444911007281 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):386-94. doi:
      10.1107/S0907444911007281. Epub 2011 Mar 18.


PMID- 15572783
OWN - NLM
STAT- MEDLINE
DA  - 20041201
DCOM- 20050222
LR  - 20141105
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 60
IP  - Pt 12 Pt 1
DP  - 2004 Dec
TI  - Developments in the CCP4 molecular-graphics project.
PG  - 2288-94
AB  - Progress towards structure determination that is both high-throughput and
      high-value is dependent on the development of integrated and automatic tools for 
      electron-density map interpretation and for the analysis of the resulting atomic 
      models. Advances in map-interpretation algorithms are extending the resolution
      regime in which fully automatic tools can work reliably, but at present human
      intervention is required to interpret poor regions of macromolecular electron
      density, particularly where crystallographic data is only available to modest
      resolution [for example, I/sigma(I) < 2.0 for minimum resolution 2.5 A]. In such 
      cases, a set of manual and semi-manual model-building molecular-graphics tools is
      needed. At the same time, converting the knowledge encapsulated in a molecular
      structure into understanding is dependent upon visualization tools, which must be
      able to communicate that understanding to others by means of both static and
      dynamic representations. CCP4 mg is a program designed to meet these needs in a
      way that is closely integrated with the ongoing development of CCP4 as a program 
      suite suitable for both low- and high-intervention computational structural
      biology. As well as providing a carefully designed user interface to advanced
      algorithms of model building and analysis, CCP4 mg is intended to present a
      graphical toolkit to developers of novel algorithms in these fields.
FAU - Potterton, Liz
AU  - Potterton L
AD  - Department of Chemistry, University of York, England. ccp4mg@ccp4.ac.uk
FAU - McNicholas, Stuart
AU  - McNicholas S
FAU - Krissinel, Eugene
AU  - Krissinel E
FAU - Gruber, Jan
AU  - Gruber J
FAU - Cowtan, Kevin
AU  - Cowtan K
FAU - Emsley, Paul
AU  - Emsley P
FAU - Murshudov, Garib N
AU  - Murshudov GN
FAU - Cohen, Serge
AU  - Cohen S
FAU - Perrakis, Anastassis
AU  - Perrakis A
FAU - Noble, Martin
AU  - Noble M
LA  - eng
GR  - B19543/Biotechnology and Biological Sciences Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20041126
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Ligands)
RN  - 0 (Nucleic Acids)
RN  - 0 (Peptide Library)
RN  - 0 (Proteins)
SB  - IM
MH  - Algorithms
MH  - *Computer Graphics
MH  - Crystallography, X-Ray
MH  - Electrons
MH  - Ligands
MH  - *Models, Molecular
MH  - Nucleic Acids/chemistry
MH  - Peptide Library
MH  - Protein Structure, Secondary
MH  - Proteins/*chemistry
MH  - Software
MH  - Static Electricity
MH  - User-Computer Interface
EDAT- 2004/12/02 09:00
MHDA- 2005/02/23 09:00
CRDT- 2004/12/02 09:00
PHST- 2004/04/21 [received]
PHST- 2004/09/22 [accepted]
PHST- 2004/11/26 [epublish]
AID - S0907444904023716 [pii]
AID - 10.1107/S0907444904023716 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2288-94. Epub 2004
      Nov 26.


PMID- 12393928
OWN - NLM
STAT- MEDLINE
DA  - 20021023
DCOM- 20030507
LR  - 20070724
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 58
IP  - Pt 11
DP  - 2002 Nov
TI  - The CCP4 molecular-graphics project.
PG  - 1955-7
AB  - This new package will provide easy-to-use access to crystallographic structure
      solution, model building and structure analysis. It will be possible for any
      developer to integrate scientific software into the system.
FAU - Potterton, Elizabeth
AU  - Potterton E
AD  - Structural Biology Laboratory, Department of Chemistry, University of York,
      Heslington, York YO10 5DD, England. lizp@ysbl.york.ac.uk
FAU - McNicholas, Stuart
AU  - McNicholas S
FAU - Krissinel, Eugene
AU  - Krissinel E
FAU - Cowtan, Kevin
AU  - Cowtan K
FAU - Noble, Martin
AU  - Noble M
LA  - eng
PT  - Journal Article
DEP - 20021021
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Macromolecular Substances)
RN  - 0 (Proteins)
SB  - IM
MH  - *Computer Graphics
MH  - Crystallography, X-Ray/*methods
MH  - Macromolecular Substances
MH  - *Models, Molecular
MH  - Proteins/chemistry
MH  - *Software
EDAT- 2002/10/24 04:00
MHDA- 2003/05/08 05:00
CRDT- 2002/10/24 04:00
PHST- 2002/05/29 [received]
PHST- 2002/08/28 [accepted]
PHST- 2002/10/21 [epublish]
AID - S0907444902015391 [pii]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1955-7. Epub 2002 Oct 21.

PMID- 18094475
OWN - NLM
STAT- MEDLINE
DA  - 20071220
DCOM- 20080331
LR  - 20140904
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 64
IP  - Pt 1
DP  - 2008 Jan
TI  - MrBUMP: an automated pipeline for molecular replacement.
PG  - 119-24
AB  - A novel automation pipeline for macromolecular structure solution by molecular
      replacement is described. There is a special emphasis on the discovery and
      preparation of a large number of search models, all of which can be passed to the
      core molecular-replacement programs. For routine molecular-replacement problems, 
      the pipeline automates what a crystallographer might do and its value is simply
      one of convenience. For more difficult cases, the pipeline aims to discover the
      particular template structure and model edits required to produce a viable search
      model and may succeed in finding an efficacious combination that would be missed 
      otherwise. An overview of MrBUMP is given and some recent additions to its
      functionality are highlighted.
FAU - Keegan, Ronan M
AU  - Keegan RM
AD  - Computational Science and Engineering Department, STFC Daresbury Laboratory,
      Daresbury, Warrington WA4 4AD, England.
FAU - Winn, Martyn D
AU  - Winn MD
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20071205
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - EC 3.6.1.- (Pyrophosphatases)
RN  - EC 3.6.1.23 (dUTP pyrophosphatase)
SB  - IM
MH  - *Algorithms
MH  - Computer Simulation
MH  - Crystallography, X-Ray
MH  - Models, Molecular
MH  - Pyrophosphatases/chemistry
MH  - *Software
PMC - PMC2394800
OID - NLM: PMC2394800
EDAT- 2007/12/21 09:00
MHDA- 2008/04/01 09:00
CRDT- 2007/12/21 09:00
PHST- 2007/05/09 [received]
PHST- 2007/07/30 [accepted]
PHST- 2007/12/05 [epublish]
AID - S0907444907037195 [pii]
AID - 10.1107/S0907444907037195 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):119-24. Epub 2007 Dec 5.

PMID- 21460441
OWN - NLM
STAT- MEDLINE
DA  - 20110404
DCOM- 20110627
LR  - 20150708
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 67
IP  - Pt 4
DP  - 2011 Apr
TI  - Overview of the CCP4 suite and current developments.
PG  - 235-42
LID - 10.1107/S0907444910045749 [doi]
AB  - The CCP4 (Collaborative Computational Project, Number 4) software suite is a
      collection of programs and associated data and software libraries which can be
      used for macromolecular structure determination by X-ray crystallography. The
      suite is designed to be flexible, allowing users a number of methods of achieving
      their aims. The programs are from a wide variety of sources but are connected by 
      a common infrastructure provided by standard file formats, data objects and
      graphical interfaces. Structure solution by macromolecular crystallography is
      becoming increasingly automated and the CCP4 suite includes several automation
      pipelines. After giving a brief description of the evolution of CCP4 over the
      last 30 years, an overview of the current suite is given. While detailed
      descriptions are given in the accompanying articles, here it is shown how the
      individual programs contribute to a complete software package.
FAU - Winn, Martyn D
AU  - Winn MD
AD  - STFC Daresbury Laboratory, Daresbury, Warrington, England. martyn.winn@stfc.ac.uk
FAU - Ballard, Charles C
AU  - Ballard CC
FAU - Cowtan, Kevin D
AU  - Cowtan KD
FAU - Dodson, Eleanor J
AU  - Dodson EJ
FAU - Emsley, Paul
AU  - Emsley P
FAU - Evans, Phil R
AU  - Evans PR
FAU - Keegan, Ronan M
AU  - Keegan RM
FAU - Krissinel, Eugene B
AU  - Krissinel EB
FAU - Leslie, Andrew G W
AU  - Leslie AG
FAU - McCoy, Airlie
AU  - McCoy A
FAU - McNicholas, Stuart J
AU  - McNicholas SJ
FAU - Murshudov, Garib N
AU  - Murshudov GN
FAU - Pannu, Navraj S
AU  - Pannu NS
FAU - Potterton, Elizabeth A
AU  - Potterton EA
FAU - Powell, Harold R
AU  - Powell HR
FAU - Read, Randy J
AU  - Read RJ
FAU - Vagin, Alexei
AU  - Vagin A
FAU - Wilson, Keith S
AU  - Wilson KS
LA  - eng
GR  - 064405/Z/01/A/Wellcome Trust/United Kingdom
GR  - 082961/Wellcome Trust/United Kingdom
GR  - BB/F020228/1/Biotechnology and Biological Sciences Research Council/United
      Kingdom
GR  - BB/F0202281/Biotechnology and Biological Sciences Research Council/United Kingdom
GR  - BB/F020384/1/Biotechnology and Biological Sciences Research Council/United
      Kingdom
GR  - BB/F020805/1/Biotechnology and Biological Sciences Research Council/United
      Kingdom
GR  - MC_G0900846/Medical Research Council/United Kingdom
GR  - MC_U105184325/Medical Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20110318
PL  - England
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Proteins)
SB  - IM
MH  - Automation, Laboratory
MH  - Cooperative Behavior
MH  - Crystallography, X-Ray/instrumentation/*methods
MH  - Proteins/*analysis
MH  - *Software Design
PMC - PMC3069738
OID - NLM: PMC3069738
EDAT- 2011/04/05 06:00
MHDA- 2011/06/28 06:00
CRDT- 2011/04/05 06:00
PHST- 2010/09/17 [received]
PHST- 2010/11/07 [accepted]
PHST- 2011/03/18 [epublish]
AID - S0907444910045749 [pii]
AID - 10.1107/S0907444910045749 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-42. doi:
      10.1107/S0907444910045749. Epub 2011 Mar 18.


PMID- 15572778
OWN - NLM
STAT- MEDLINE
DA  - 20041201
DCOM- 20050222
LR  - 20141105
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 60
IP  - Pt 12 Pt 1
DP  - 2004 Dec
TI  - The new CCP4 Coordinate Library as a toolkit for the design of coordinate-related
      applications in protein crystallography.
PG  - 2250-5
AB  - The new CCP4 Coordinate Library is a development aiming to provide a common layer
      of coordinate-related functionality to the existing applications in the CCP4
      suite, as well as a variety of tools that can simplify the design of new
      applications where they relate to atomic coordinates. The Library comprises a
      wide spectrum of useful functions, ranging from parsing coordinate formats and
      elementary editing operations on the coordinate hierarchy of biomolecules, to
      high-level functionality such as calculation of secondary structure, interatomic 
      bonds, atomic contacts, symmetry transformations, structure superposition and
      many others. Most of the functions are available in a C++ object interface;
      however, a Fortran interface is provided for compatibility with older CCP4
      applications. The paper describes the general principles of the Library design
      and the most important functionality. The Library, together with documentation,
      is available under the LGPL license from the CCP4 suite version 5.0 and higher.
FAU - Krissinel, E B
AU  - Krissinel EB
AD  - European Bioinformatics Institute, Genome Campus, Hinxton, Cambridge CB10 1SD,
      England. keb@ebi.ac.uk
FAU - Winn, M D
AU  - Winn MD
FAU - Ballard, C C
AU  - Ballard CC
FAU - Ashton, A W
AU  - Ashton AW
FAU - Patel, P
AU  - Patel P
FAU - Potterton, E A
AU  - Potterton EA
FAU - McNicholas, S J
AU  - McNicholas SJ
FAU - Cowtan, K D
AU  - Cowtan KD
FAU - Emsley, P
AU  - Emsley P
LA  - eng
GR  - B19543/Biotechnology and Biological Sciences Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20041126
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Proteins)
SB  - IM
MH  - Computer Graphics
MH  - Crystallography, X-Ray/*statistics & numerical data
MH  - Databases, Protein
MH  - Models, Molecular
MH  - Protein Conformation
MH  - Proteins/*chemistry
MH  - *Software
MH  - User-Computer Interface
EDAT- 2004/12/02 09:00
MHDA- 2005/02/23 09:00
CRDT- 2004/12/02 09:00
PHST- 2004/01/08 [received]
PHST- 2004/10/25 [accepted]
PHST- 2004/11/26 [epublish]
AID - S0907444904027167 [pii]
AID - 10.1107/S0907444904027167 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2250-5. Epub 2004
      Nov 26.