PHENIX protocols

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


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


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

Additional information

Publications for Python-based Hierarchical ENvironment for Integrated Xtallography

PHENIX IN pipelines

PMCID: 5913616
PMID: 29394369
DOI: 10.1093/jxb/ery036

[…] ligand was built into the positive difference density appearing at the 3.0 sigma level followed by 10 cycles of maximum likelihood restrained refinement in refmac5 (murshudov et al., 2011) or phenix (adams et al., 2010). during this operation, care was taken to use the programs and scripts of the originators, as described in the respective pdb header., the figures were created […]

PMCID: 5370187
PMID: 28347402
DOI: 10.7554/eLife.21465.039

[…] the sad method from peak-data collected from semet crystals. the crank2 pipeline (skubák and pannu, 2013) was used for structure solution and initial model building. refinement was carried out with phenix (adams et al., 2010) (rrid:scr_014224). data collection and refinement statistics are summarized in supplementary file 1. all figures representing crystal structures were prepared using pymol […]

PMCID: 5087735
PMID: 27634042
DOI: 10.1074/jbc.M116.721894

[…] 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 = […]

PMCID: 4681132
PMID: 26605533
DOI: 10.1038/nature16143

[…] improve the model after initial model building, we performed automated real-space coordinate refinement against the elongating pol iii density map using a scripted workflow based on ccp4 and cctbx/phenix libraries64,65. the sharpened experimental density map of elongating pol iii was used as the refinement target. due to the resolution differences in the map we initially performed refinement […]

PMCID: 4681132
PMID: 26605533
DOI: 10.1038/nature16143

[…] pixel size. coordinate refinement was performed by geometry-restrained real-space refinement based on gradient-driven minimization of a combined map and restraint target as implemented in cctbx/phenix up to the computed local mean resolution of each subunit. grid searches were employed for automated identification of optimal refinement weights to balance the relative contribution […]

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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