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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


No version available



  • person_outline Paul Adams
  • person_outline Pavel Afonine

Additional information

Publications for Python-based Hierarchical ENvironment for Integrated Xtallography

PHENIX citations


Activity of acetyltransferase toxins involved in Salmonella persister formation during macrophage infection

Nat Commun
PMCID: 5959882
PMID: 29777131
DOI: 10.1038/s41467-018-04472-6
call_split See protocol

[…] en. Diffraction data were acquired at diamond light source (Oxfordshire, UK) on beamline I04–1. High-resolution native data sets were auto-integrated using autoPROC software. Phases was obtained with PHENIX Phaser software using molecular replacement function and a polyalanine scaffold of TacT (PDB 5FVJ) as a model. The model was then modified using AutoBuild and manually improved using Coot and r […]


X ray structure of a carpet like antimicrobial defensin–phospholipid membrane disruption complex

Nat Commun
PMCID: 5958116
PMID: 29773800
DOI: 10.1038/s41467-018-04434-y
call_split See protocol

[…] cessed using XDS. The structure was solved by molecular replacement with PHASER using the structure of NaD1 in its dimeric form as a search model. The final model was built with Coot and refined with Phenix to a resolution of 2.5 Å with the final Rwork and Rfree values of 0.2031 and 0.2519, respectively. All data collection and refinement statistics are summarized in Table . All programs were acce […]


Structure of a cleavage independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer

Nat Commun
PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] l using Phaser. The BG505 NFL.664+PGV19+PGT122 complex structure was determined by MR with PGV19 (determined in this study) and BG505 SOSIP.664+PGT122 from PDB 4TVP. The structures were refined using Phenix and model building performed in Coot. MolProbity, Privateer, and pdb-care were used for structure validation. The refinement statistics are reported in Supplementary Table . […]


Structural basis for the recognition of complex type N glycans by Endoglycosidase S

Nat Commun
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] ture determination of EndoSD233AE235L-G2 was resolved using as a template the previously reported EndoS structure (unmodified PDB 4NUZ) and molecular replacement methods implemented in Phaser and the PHENIX suite. Model rebuilding was carried out with Buccaneer and the CCP4 suite. The final manual building was performed with Coot and refinement with phenix.refine. The structure was validated by Mo […]


Vaccine elicited receptor binding site antibodies neutralize two New World hemorrhagic fever arenaviruses

Nat Commun
PMCID: 5951886
PMID: 29760382
DOI: 10.1038/s41467-018-04271-z
call_split See protocol

[…] y molecular replacement with PHASER with MACV GP1 (PBD: 2WFO) and the unliganded CR1-07 Fab as a search models. For all structures, we performed iterative model building with COOT and refinement with PHENIX and/or BUSTER. For both the CR1-10 Fab/JUNV GP1/CR1-28 Fab and the MACV GP1/CR1-07 Fab complex, four copies of the complex were identified per ASU, allowing for electron density modification fo […]


Structural basis for cofilin binding and actin filament disassembly

Nat Commun
PMCID: 5945598
PMID: 29749375
DOI: 10.1038/s41467-018-04290-w
call_split See protocol

[…] atoms except hydrogens, and the solvent effect was modeled with Generalized Born implicit solvent. After the cascade-MDFF calculation converged, Ramachandran outliers were fixed and refined with the phenix.real_space_refine program. The resulting model was iteratively refined using COOT, MDFF and phenix.real_space_refine. After convergence, histidine 73 was replaced by a methylated-histidine. […]


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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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