PHENIX pipeline

PHENIX specifications


Unique identifier OMICS_06371
Alternative name Python-based Hierarchical ENvironment for Integrated Xtallography
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Medium
Version 1.13
Stability Stable
Registration required Yes
Maintained Yes


  • phenix.real_space_refine
  • phenix.polder
  • phenix.xtriage
  • eLBOW
  • Phaser-MR
  • AutoSol
  • LigandFit


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  • person_outline Paul Adams <>
  • person_outline Pavel Afonine <>

Additional information

Publications for Python-based Hierarchical ENvironment for Integrated Xtallography

PHENIX citations

PMCID: 5430744

[…] using the hkl-2000 program50. the structure was determined through molecular replacement method with the molrep program51 in the ccp4 program package. structure refinement was conducted using the phenix refine program in the phenix program package52. after each refinement cycle, the model was adjusted manually with the wincoot program53. r work/r free values of smon0123 (n-18/c-5)/c∆0s, […]

PMCID: 5087735

[…] using unknown protein from b. thetaiotaomicron as a model (pdb code 2fg1) obtained by phyre2 (70). initial model was improved by several cycles of refinement, using programs refmac (71, 72) and phenix (73). data collection and refinement statistics are given in table 1. final coordinates and structure factors have been deposited in the protein data bank (accession number 5e3b)., a rmerge = […]

PHENIX institution(s)
Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA; New Mexico Consortium, Los Alamos, NM, USA; Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM-UdS, Illkirch, France; Université de Lorraine, Faculté des Sciences et Technologies, Vandoeuvre-les-Nancy, France; Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
PHENIX funding source(s)
Supported by the NIH (grant GM063210) and the Phenix Industrial Consortium, in part by the US Department of Energy under Contract No. DE-AC02-05CH11231, the French Infrastructure for Integrated Structural Biology FRISBI ANR-10- INBS-05 and of Instruct-ERIC and by a Principal Research Fellowship funded by the Wellcome Trust (Grant 082961/ Z/07/Z).

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