Graphical tools for macromolecular crystallography in PHENIX

被引:125
作者
Echols, Nathaniel [1 ]
Grosse-Kunstleve, Ralf W. [1 ]
Afonine, Pavel V. [1 ]
Bunkoczi, Gabor [2 ]
Chen, Vincent B. [3 ]
Headd, Jeffrey J. [1 ]
McCoy, Airlie J. [2 ]
Moriarty, Nigel W. [1 ]
Read, Randy J. [2 ]
Richardson, David C. [3 ]
Richardson, Jane S. [3 ]
Terwilliger, Thomas C. [4 ]
Adams, Paul D. [1 ,5 ]
机构
[1] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA
[2] Univ Cambridge, Cambridge Inst Med Res, Dept Haematol, Cambridge CB2 0XY, England
[3] Duke Univ, Med Ctr, Dept Biochem, Durham, NC 27710 USA
[4] Los Alamos Natl Lab, Los Alamos, NM 87545 USA
[5] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA
来源
JOURNAL OF APPLIED CRYSTALLOGRAPHY | 2012年 / 45卷
关键词
PROTEIN DATA-BANK; MOLECULAR-REPLACEMENT; STRUCTURE REFINEMENT; MODEL; VALIDATION; PROGRAM; DENSITY; QUALITY;
D O I
10.1107/S0021889812017293
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
A new Python-based graphical user interface for the PHENIX suite of crystallography software is described. This interface unifies the command-line programs and their graphical displays, simplifying the development of new interfaces and avoiding duplication of function. With careful design, graphical interfaces can be displayed automatically, instead of being manually constructed. The resulting package is easily maintained and extended as new programs are added or modified.
引用
收藏
页码:581 / 586
页数:6
相关论文
共 42 条
  • [31] A graphical user interface to the CCP4 program suite
    Potterton, E
    Briggs, P
    Turkenburg, M
    Dodson, E
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2003, 59 : 1131 - 1137
  • [32] Robust indexing for automatic data collection
    Sauter, NK
    Grosse-Kunstleve, RW
    Adams, PD
    [J]. JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2004, 37 : 399 - 409
  • [33] The VMD-XPLOR visualization package for NMR structure refinement
    Schwieters, CD
    Clore, GM
    [J]. JOURNAL OF MAGNETIC RESONANCE, 2001, 149 (02) : 239 - 244
  • [34] Stroustrup Bjarne, 2000, The C++ Programming Language
  • [35] Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
    Terwilliger, Thomas C.
    Grosse-Kunstleve, Ralf W.
    Afonine, Pavel V.
    Moriarty, Nigel W.
    Zwart, Peter H.
    Hung, Li-Wei
    Read, Randy J.
    Adams, Paul D.
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2008, 64 : 61 - 69
  • [36] Automated ligand fitting by core-fragment fitting and extension into density
    Terwilliger, Thomas C.
    Klei, Herbert
    Adams, Paul D.
    Moriarty, Nigel W.
    Cohn, Judith D.
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2006, 62 : 915 - 922
  • [37] Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    Terwilliger, Thomas C.
    Adams, Paul D.
    Read, Randy J.
    McCoy, Airlie J.
    Moriarty, Nigel W.
    Grosse-Kunstleve, Ralf W.
    Afonine, Pavel V.
    Zwart, Peter H.
    Hung, Li-Wei
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2009, 65 : 582 - 601
  • [38] Crystallographic model quality at a glance
    Urzhumtseva, Ludmila
    Afonine, Pavel V.
    Adams, Paul D.
    Urzhumtsev, Alexandre
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2009, 65 : 297 - 300
  • [39] Van Rossum G., 2003, An introduction to Python
  • [40] Vonrhein Clemens, 2007, Methods Mol Biol, V364, P215, DOI 10.1385/1-59745-266-1:215