PHENIX protocols

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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


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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: 5799190
PMID: 29403017
DOI: 10.1038/s41598-018-20107-8

[…] source, argonne national laboratory. data were processed using xds. the apo t. thermophilus 70s ribosome from pdb code 4v51 was used as the starting model. refinement was carried out using cns and phenix. the ligands including mrna, e-trna and partial p-trna without the cca-end, and partial rf2 without the ggq motif were first built into unbiased difference density. after the refinement, […]

PMCID: 5803273
PMID: 29416037
DOI: 10.1038/s41467-018-02996-5

[…] table . the solvent content was analyzed using the program rwcontents in the ccp4 suite. to check the absence of significant model bias, a composite omit map was created using the software suite phenix (supplementary figure ). figures were produced using the software pymol (the pymol molecular graphics system, version 1.1, delano scientific llc)., to determine the evolution of the structural […]

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

[…] relevant cases a suitable 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 () or phenix (). 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 with ‘pymol’ (version […]

PMCID: 5216409
PMID: 28059088
DOI: 10.1038/srep39392

[…] in ). the datasets were indexed and integrated using xds and combined and scaled using aimless in ccp4. experimental phases, a density modified map and an initial model were calculated using autosol in phenix, with one molecule in the asymmetric unit and two zinc sites identified. figure of merits were 0.31 and 0.66, before and after density modification. the model was further built […]

PMCID: 5270246
PMID: 28128331
DOI: 10.1038/srep41487

[…] program phaser was used for molecular replacement (, with the pparγ-rosi structure (pbd code: 1fm6) as a search model. the initial model was manually built and refined with the phenix program package. all figures were prepared using pymol (delano scientific, san carlos, ca,, how to cite this article: yi, w. et al. identification of a novel selective […]

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PHENIX in publications

PMCID: 5959882
PMID: 29777131
DOI: 10.1038/s41467-018-04472-6

[…] 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 […]

PMCID: 5958116
PMID: 29773800
DOI: 10.1038/s41467-018-04434-y

[…] 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 […]

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

[…] 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 ., the sec-purified […]

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

[…] 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 […]

PMCID: 5951886
PMID: 29760382
DOI: 10.1038/s41467-018-04271-z

[…] 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 […]

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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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