We are analyzing https://link.springer.com/protocol/10.1007/978-1-60327-058-8_28.

Title:
Automated Structure Solution with the PHENIX Suite | SpringerLink
Description:
Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce...
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Keywords {🔍}

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Topics {✒️}

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Schema {🗺️}

ScholarlyArticle:
      headline:Automated Structure Solution with the PHENIX Suite
      pageEnd:435
      pageStart:419
      image:https://media.springernature.com/w153/springer-static/cover/book/978-1-60327-058-8.jpg
      genre:
         Springer Protocols
      isPartOf:
         name:Structural Proteomics
         isbn:
            978-1-60327-058-8
            978-1-58829-809-6
         type:Book
      publisher:
         name:Humana Press
         logo:
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      author:
            name:Peter H. Zwart
            affiliation:
                  name:Lawrence Berkeley National Laboratory
                  address:
                     name:Lawrence Berkeley National Laboratory, Berkeley, California
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Pavel V. Afonine
            affiliation:
                  name:Lawrence Berkeley National Laboratory
                  address:
                     name:Lawrence Berkeley National Laboratory, Berkeley, California
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Ralf W. Grosse-Kunstleve
            affiliation:
                  name:Lawrence Berkeley National Laboratory
                  address:
                     name:Lawrence Berkeley National Laboratory, Berkeley, California
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Li-Wei Hung
            affiliation:
                  name:Biophysics Group, Los Alamos National Laboratory
                  address:
                     name:Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Thomas R. Ioerger
            affiliation:
                  name:Texas A&M University
                  address:
                     name:Department of Computer Science, Texas A&M University, College Hill, Texas
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Airlie J. McCoy
            affiliation:
                  name:University of Cambridge, Cambridge Institute for Medical Research
                  address:
                     name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Erik McKee
            affiliation:
                  name:Texas A&M University
                  address:
                     name:Department of Computer Science, Texas A&M University, College Hill, Texas
                     type:PostalAddress
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            type:Person
            name:Nigel W. Moriarty
            affiliation:
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                  address:
                     name:Lawrence Berkeley National Laboratory, Berkeley, California
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            name:Randy J. Read
            affiliation:
                  name:University of Cambridge, Cambridge Institute for Medical Research
                  address:
                     name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
                     type:PostalAddress
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            type:Person
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            affiliation:
                  name:Texas A&M University
                  address:
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                     type:PostalAddress
                  type:Organization
            type:Person
            name:Nicholas K. Sauter
            affiliation:
                  name:Lawrence Berkeley National Laboratory
                  address:
                     name:Lawrence Berkeley National Laboratory, Berkeley, California
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Laurent C. Storoni
            affiliation:
                  name:University of Cambridge, Cambridge Institute for Medical Research
                  address:
                     name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Thomas C. Terwilliger
            affiliation:
                  name:Los Alamos National Laboratory
                  address:
                     name:Biophysics Division, Los Alamos National Laboratory, Los Alamos, New Mexico
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Paul D. Adams
            affiliation:
                  name:University of California
                  address:
                     name:Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, and Department of Chemistry, University of California, Berkeley, California
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      keywords:Cholic Acid, Density Modification, Molecular Replacement, Command Line Interface, Atomic Displacement Parameter
      description:Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.
      datePublished:2008
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Book:
      name:Structural Proteomics
      isbn:
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         978-1-58829-809-6
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      name:Humana Press
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      name:Lawrence Berkeley National Laboratory
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         name:Lawrence Berkeley National Laboratory, Berkeley, California
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      address:
         name:Lawrence Berkeley National Laboratory, Berkeley, California
         type:PostalAddress
      name:Biophysics Group, Los Alamos National Laboratory
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         name:Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
         type:PostalAddress
      name:Texas A&M University
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         name:Department of Computer Science, Texas A&M University, College Hill, Texas
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      name:University of Cambridge, Cambridge Institute for Medical Research
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         name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
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         name:Department of Computer Science, Texas A&M University, College Hill, Texas
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         name:Lawrence Berkeley National Laboratory, Berkeley, California
         type:PostalAddress
      name:University of Cambridge, Cambridge Institute for Medical Research
      address:
         name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
         type:PostalAddress
      name:Texas A&M University
      address:
         name:Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
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         name:Lawrence Berkeley National Laboratory, Berkeley, California
         type:PostalAddress
      name:University of Cambridge, Cambridge Institute for Medical Research
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         name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
         type:PostalAddress
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         name:Biophysics Division, Los Alamos National Laboratory, Los Alamos, New Mexico
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            name:Lawrence Berkeley National Laboratory
            address:
               name:Lawrence Berkeley National Laboratory, Berkeley, California
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            name:Lawrence Berkeley National Laboratory
            address:
               name:Lawrence Berkeley National Laboratory, Berkeley, California
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      affiliation:
            name:Biophysics Group, Los Alamos National Laboratory
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            name:Texas A&M University
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               type:PostalAddress
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      name:Airlie J. McCoy
      affiliation:
            name:University of Cambridge, Cambridge Institute for Medical Research
            address:
               name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
               type:PostalAddress
            type:Organization
      name:Erik McKee
      affiliation:
            name:Texas A&M University
            address:
               name:Department of Computer Science, Texas A&M University, College Hill, Texas
               type:PostalAddress
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      name:Nigel W. Moriarty
      affiliation:
            name:Lawrence Berkeley National Laboratory
            address:
               name:Lawrence Berkeley National Laboratory, Berkeley, California
               type:PostalAddress
            type:Organization
      name:Randy J. Read
      affiliation:
            name:University of Cambridge, Cambridge Institute for Medical Research
            address:
               name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
               type:PostalAddress
            type:Organization
      name:James C. Sacchettini
      affiliation:
            name:Texas A&M University
            address:
               name:Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
               type:PostalAddress
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      name:Nicholas K. Sauter
      affiliation:
            name:Lawrence Berkeley National Laboratory
            address:
               name:Lawrence Berkeley National Laboratory, Berkeley, California
               type:PostalAddress
            type:Organization
      name:Laurent C. Storoni
      affiliation:
            name:University of Cambridge, Cambridge Institute for Medical Research
            address:
               name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
               type:PostalAddress
            type:Organization
      name:Thomas C. Terwilliger
      affiliation:
            name:Los Alamos National Laboratory
            address:
               name:Biophysics Division, Los Alamos National Laboratory, Los Alamos, New Mexico
               type:PostalAddress
            type:Organization
      name:Paul D. Adams
      affiliation:
            name:University of California
            address:
               name:Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, and Department of Chemistry, University of California, Berkeley, California
               type:PostalAddress
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      name:Lawrence Berkeley National Laboratory, Berkeley, California
      name:Lawrence Berkeley National Laboratory, Berkeley, California
      name:Lawrence Berkeley National Laboratory, Berkeley, California
      name:Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
      name:Department of Computer Science, Texas A&M University, College Hill, Texas
      name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
      name:Department of Computer Science, Texas A&M University, College Hill, Texas
      name:Lawrence Berkeley National Laboratory, Berkeley, California
      name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
      name:Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
      name:Lawrence Berkeley National Laboratory, Berkeley, California
      name:Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
      name:Biophysics Division, Los Alamos National Laboratory, Los Alamos, New Mexico
      name:Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, and Department of Chemistry, University of California, Berkeley, California
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