Software:Article Title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death.
Article Snippet: .. Software and code Policy information about availability of computer code Data collection NMR: Topspin version 4.1.3 (Bruker Biospin); MD: GROMACS 2020/2021; STORM: Nikon NIS elements version 5.30; Cell biology: Fusion Solo S, Gen5, Zen Blue 2.3 Imaging Software; Negative Stain TEM: iTEM Build 5.2, Cryo-EM: Titan Krios electron microscope (FEI) with GIF Quantum LS Imaging filter (Gatan) and K2 summit (Gatan) operated using SerialEM 3.8.3; SparkControl v2.3 Data analysis NMR: CCPN version 3.0.4, xmgrace version Grace 5.1.25; MD: GROMACS 2020/2021, R version 3.6.3, PyMol 2.5.0; STORM: Data analysis: Decode v0.1, Matlab 2020b, Fiji with ImageJ 1.53q, ThunderSTORM v1.3, own custom processing codes (https://github.com/christian-7/); Cell biology: Microsoft Excel for Mac v16, Prism Graphpad 9.0, Gen5, FiJi, Zen Blue 2.3 Imaging Software; Structural Biology: Phenix Version 1.19.2-4158; Coot 0.8.9.2 EL, 0.9.7 EL; cryoSPARC v3.2, v3.3.2; ChimeraX v1.2.5,1.3, Alphafold 2.2.0, EvCouplings V2 webserver, MolProbity v4.5.2 Webserver For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Nuclear Magnetic Resonance:Article Title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death.
Article Snippet: .. Software and code Policy information about availability of computer code Data collection NMR: Topspin version 4.1.3 (Bruker Biospin); MD: GROMACS 2020/2021; STORM: Nikon NIS elements version 5.30; Cell biology: Fusion Solo S, Gen5, Zen Blue 2.3 Imaging Software; Negative Stain TEM: iTEM Build 5.2, Cryo-EM: Titan Krios electron microscope (FEI) with GIF Quantum LS Imaging filter (Gatan) and K2 summit (Gatan) operated using SerialEM 3.8.3; SparkControl v2.3 Data analysis NMR: CCPN version 3.0.4, xmgrace version Grace 5.1.25; MD: GROMACS 2020/2021, R version 3.6.3, PyMol 2.5.0; STORM: Data analysis: Decode v0.1, Matlab 2020b, Fiji with ImageJ 1.53q, ThunderSTORM v1.3, own custom processing codes (https://github.com/christian-7/); Cell biology: Microsoft Excel for Mac v16, Prism Graphpad 9.0, Gen5, FiJi, Zen Blue 2.3 Imaging Software; Structural Biology: Phenix Version 1.19.2-4158; Coot 0.8.9.2 EL, 0.9.7 EL; cryoSPARC v3.2, v3.3.2; ChimeraX v1.2.5,1.3, Alphafold 2.2.0, EvCouplings V2 webserver, MolProbity v4.5.2 Webserver For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Imaging:Article Title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death.
Article Snippet: .. Software and code Policy information about availability of computer code Data collection NMR: Topspin version 4.1.3 (Bruker Biospin); MD: GROMACS 2020/2021; STORM: Nikon NIS elements version 5.30; Cell biology: Fusion Solo S, Gen5, Zen Blue 2.3 Imaging Software; Negative Stain TEM: iTEM Build 5.2, Cryo-EM: Titan Krios electron microscope (FEI) with GIF Quantum LS Imaging filter (Gatan) and K2 summit (Gatan) operated using SerialEM 3.8.3; SparkControl v2.3 Data analysis NMR: CCPN version 3.0.4, xmgrace version Grace 5.1.25; MD: GROMACS 2020/2021, R version 3.6.3, PyMol 2.5.0; STORM: Data analysis: Decode v0.1, Matlab 2020b, Fiji with ImageJ 1.53q, ThunderSTORM v1.3, own custom processing codes (https://github.com/christian-7/); Cell biology: Microsoft Excel for Mac v16, Prism Graphpad 9.0, Gen5, FiJi, Zen Blue 2.3 Imaging Software; Structural Biology: Phenix Version 1.19.2-4158; Coot 0.8.9.2 EL, 0.9.7 EL; cryoSPARC v3.2, v3.3.2; ChimeraX v1.2.5,1.3, Alphafold 2.2.0, EvCouplings V2 webserver, MolProbity v4.5.2 Webserver For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Staining:Article Title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death.
Article Snippet: .. Software and code Policy information about availability of computer code Data collection NMR: Topspin version 4.1.3 (Bruker Biospin); MD: GROMACS 2020/2021; STORM: Nikon NIS elements version 5.30; Cell biology: Fusion Solo S, Gen5, Zen Blue 2.3 Imaging Software; Negative Stain TEM: iTEM Build 5.2, Cryo-EM: Titan Krios electron microscope (FEI) with GIF Quantum LS Imaging filter (Gatan) and K2 summit (Gatan) operated using SerialEM 3.8.3; SparkControl v2.3 Data analysis NMR: CCPN version 3.0.4, xmgrace version Grace 5.1.25; MD: GROMACS 2020/2021, R version 3.6.3, PyMol 2.5.0; STORM: Data analysis: Decode v0.1, Matlab 2020b, Fiji with ImageJ 1.53q, ThunderSTORM v1.3, own custom processing codes (https://github.com/christian-7/); Cell biology: Microsoft Excel for Mac v16, Prism Graphpad 9.0, Gen5, FiJi, Zen Blue 2.3 Imaging Software; Structural Biology: Phenix Version 1.19.2-4158; Coot 0.8.9.2 EL, 0.9.7 EL; cryoSPARC v3.2, v3.3.2; ChimeraX v1.2.5,1.3, Alphafold 2.2.0, EvCouplings V2 webserver, MolProbity v4.5.2 Webserver For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Transmission Electron Microscopy:Article Title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death.
Article Snippet: .. Software and code Policy information about availability of computer code Data collection NMR: Topspin version 4.1.3 (Bruker Biospin); MD: GROMACS 2020/2021; STORM: Nikon NIS elements version 5.30; Cell biology: Fusion Solo S, Gen5, Zen Blue 2.3 Imaging Software; Negative Stain TEM: iTEM Build 5.2, Cryo-EM: Titan Krios electron microscope (FEI) with GIF Quantum LS Imaging filter (Gatan) and K2 summit (Gatan) operated using SerialEM 3.8.3; SparkControl v2.3 Data analysis NMR: CCPN version 3.0.4, xmgrace version Grace 5.1.25; MD: GROMACS 2020/2021, R version 3.6.3, PyMol 2.5.0; STORM: Data analysis: Decode v0.1, Matlab 2020b, Fiji with ImageJ 1.53q, ThunderSTORM v1.3, own custom processing codes (https://github.com/christian-7/); Cell biology: Microsoft Excel for Mac v16, Prism Graphpad 9.0, Gen5, FiJi, Zen Blue 2.3 Imaging Software; Structural Biology: Phenix Version 1.19.2-4158; Coot 0.8.9.2 EL, 0.9.7 EL; cryoSPARC v3.2, v3.3.2; ChimeraX v1.2.5,1.3, Alphafold 2.2.0, EvCouplings V2 webserver, MolProbity v4.5.2 Webserver For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Cryo-EM Sample Prep:Article Title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death.
Article Snippet: .. Software and code Policy information about availability of computer code Data collection NMR: Topspin version 4.1.3 (Bruker Biospin); MD: GROMACS 2020/2021; STORM: Nikon NIS elements version 5.30; Cell biology: Fusion Solo S, Gen5, Zen Blue 2.3 Imaging Software; Negative Stain TEM: iTEM Build 5.2, Cryo-EM: Titan Krios electron microscope (FEI) with GIF Quantum LS Imaging filter (Gatan) and K2 summit (Gatan) operated using SerialEM 3.8.3; SparkControl v2.3 Data analysis NMR: CCPN version 3.0.4, xmgrace version Grace 5.1.25; MD: GROMACS 2020/2021, R version 3.6.3, PyMol 2.5.0; STORM: Data analysis: Decode v0.1, Matlab 2020b, Fiji with ImageJ 1.53q, ThunderSTORM v1.3, own custom processing codes (https://github.com/christian-7/); Cell biology: Microsoft Excel for Mac v16, Prism Graphpad 9.0, Gen5, FiJi, Zen Blue 2.3 Imaging Software; Structural Biology: Phenix Version 1.19.2-4158; Coot 0.8.9.2 EL, 0.9.7 EL; cryoSPARC v3.2, v3.3.2; ChimeraX v1.2.5,1.3, Alphafold 2.2.0, EvCouplings V2 webserver, MolProbity v4.5.2 Webserver For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
Microscopy:Article Title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death.
Article Snippet: .. Software and code Policy information about availability of computer code Data collection NMR: Topspin version 4.1.3 (Bruker Biospin); MD: GROMACS 2020/2021; STORM: Nikon NIS elements version 5.30; Cell biology: Fusion Solo S, Gen5, Zen Blue 2.3 Imaging Software; Negative Stain TEM: iTEM Build 5.2, Cryo-EM: Titan Krios electron microscope (FEI) with GIF Quantum LS Imaging filter (Gatan) and K2 summit (Gatan) operated using SerialEM 3.8.3; SparkControl v2.3 Data analysis NMR: CCPN version 3.0.4, xmgrace version Grace 5.1.25; MD: GROMACS 2020/2021, R version 3.6.3, PyMol 2.5.0; STORM: Data analysis: Decode v0.1, Matlab 2020b, Fiji with ImageJ 1.53q, ThunderSTORM v1.3, own custom processing codes (https://github.com/christian-7/); Cell biology: Microsoft Excel for Mac v16, Prism Graphpad 9.0, Gen5, FiJi, Zen Blue 2.3 Imaging Software; Structural Biology: Phenix Version 1.19.2-4158; Coot 0.8.9.2 EL, 0.9.7 EL; cryoSPARC v3.2, v3.3.2; ChimeraX v1.2.5,1.3, Alphafold 2.2.0, EvCouplings V2 webserver, MolProbity v4.5.2 Webserver For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors and reviewers. ..
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