Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor
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{"title"=>"Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor", "type"=>"journal", "authors"=>[{"first_name"=>"Manuel", "last_name"=>"Wahle", "scopus_author_id"=>"36992669500"}, {"first_name"=>"Willy", "last_name"=>"Wriggers", "scopus_author_id"=>"7004454996"}], "year"=>2015, "source"=>"PLoS Computational Biology", "identifiers"=>{"doi"=>"10.1371/journal.pcbi.1004516", "issn"=>"15537358", "sgr"=>"84946035136", "pmid"=>"26505203", "pui"=>"606741300", "scopus"=>"2-s2.0-84946035136"}, "id"=>"b4997bf8-720a-3dd7-bab5-e23511b6ea31", "abstract"=>"The modeling of large biomolecular assemblies relies on an efficient rendering of their hierarchical architecture across a wide range of spatial level of detail. We describe a paradigm shift currently under way in computer graphics towards the use of more realistic global illumination models, and we apply the so-called ambient occlusion approach to our open-source multi-scale modeling program, Sculptor. While there are many other higher quality global illumination approaches going all the way up to full GPU-accelerated ray tracing, they do not provide size-specificity of the features they shade. Ambient occlusion is an aspect of global lighting that offers great visual benefits and powerful user customization. By estimating how other molecular shape features affect the reception of light at some surface point, it effectively simulates indirect shadowing. This effect occurs between molecular surfaces that are close to each other, or in pockets such as protein or ligand binding sites. By adding ambient occlusion, large macromolecular systems look much more natural, and the perception of characteristic surface features is strongly enhanced. In this work, we present a real-time implementation of screen space ambient occlusion that delivers realistic cues about tunable spatial scale characteristics of macromolecular architecture. Heretofore, the visualization of large biomolecular systems, comprising e.g. hundreds of thousands of atoms or Mega-Dalton size electron microscopy maps, did not take into account the length scales of interest or the spatial resolution of the data. Our approach has been uniquely customized with shading that is tuned for pockets and cavities of a user-defined size, making it useful for visualizing molecular features at multiple scales of interest. This is a feature that none of the conventional ambient occlusion approaches provide. Actual Sculptor screen shots illustrate how our implementation supports the size-dependent rendering of molecular surface features.", "link"=>"http://www.mendeley.com/research/multiscale-visualization-molecular-architecture-using-realtime-ambient-occlusion-sculptor", "reader_count"=>7, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>3, "Professor"=>1, "Student > Master"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>3, "Professor"=>1, "Student > Master"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>2, "Physics and Astronomy"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2381112"], "description"=>"<p>Shown is a composite of CCMV images (PDB ID 1CWP) with three different heuristic sampling diameter settings. Adaption of the diameter highlights structural arrangements on different scales.</p>", "links"=>[], "tags"=>["ambient occlusion approaches", "surface features", "Actual Sculptor screen shots", "screen space ambient occlusion", "ambient occlusion approach", "ligand binding sites"], "article_id"=>1586114, "categories"=>["Uncategorised"], "users"=>["Manuel Wahle", "Willy Wriggers"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004516.g007", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Three_way_comparison_of_sampling_size_effect_/1586114", "title"=>"Three-way comparison of sampling size effect.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-27 03:06:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/2381113"], "description"=>"<div><p>The modeling of large biomolecular assemblies relies on an efficient rendering of their hierarchical architecture across a wide range of spatial level of detail. We describe a paradigm shift currently under way in computer graphics towards the use of more realistic global illumination models, and we apply the so-called ambient occlusion approach to our open-source multi-scale modeling program, Sculptor. While there are many other higher quality global illumination approaches going all the way up to full GPU-accelerated ray tracing, they do not provide size-specificity of the features they shade. Ambient occlusion is an aspect of global lighting that offers great visual benefits and powerful user customization. By estimating how other molecular shape features affect the reception of light at some surface point, it effectively simulates indirect shadowing. This effect occurs between molecular surfaces that are close to each other, or in pockets such as protein or ligand binding sites. By adding ambient occlusion, large macromolecular systems look much more natural, and the perception of characteristic surface features is strongly enhanced. In this work, we present a real-time implementation of screen space ambient occlusion that delivers realistic cues about tunable spatial scale characteristics of macromolecular architecture. Heretofore, the visualization of large biomolecular systems, comprising e.g. hundreds of thousands of atoms or Mega-Dalton size electron microscopy maps, did not take into account the length scales of interest or the spatial resolution of the data. Our approach has been uniquely customized with shading that is tuned for pockets and cavities of a user-defined size, making it useful for visualizing molecular features at multiple scales of interest. This is a feature that none of the conventional ambient occlusion approaches provide. Actual Sculptor screen shots illustrate how our implementation supports the size-dependent rendering of molecular surface features.</p></div>", "links"=>[], "tags"=>["ambient occlusion approaches", "surface features", "Actual Sculptor screen shots", "screen space ambient occlusion", "ambient occlusion approach", "ligand binding sites"], "article_id"=>1586116, "categories"=>["Uncategorised"], "users"=>["Manuel Wahle", "Willy Wriggers"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004516", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multi_scale_Visualization_of_Molecular_Architecture_Using_Real_Time_Ambient_Occlusion_in_Sculptor_/1586116", "title"=>"Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-27 03:06:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/2381083"], "description"=>"<p>(a) Standard local lighting, which provides only a locally acceptable approximation of real world lighting. (b) Depth cueing, which unevenly shades the three (slightly tilted) channels and looks unrealistic at the bottom. (c-d) SSAO, at two different sampling sizes that emphasize spatial features according to user preference. The protein is shown in van der Waals mode in an orientation corresponding to Fig 2 in [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004516#pcbi.1004516.ref016\" target=\"_blank\">16</a>]. All molecular graphics figures in this paper were created with Sculptor version 2.1 [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004516#pcbi.1004516.ref017\" target=\"_blank\">17</a>, <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004516#pcbi.1004516.ref018\" target=\"_blank\">18</a>].</p>", "links"=>[], "tags"=>["ambient occlusion approaches", "surface features", "Actual Sculptor screen shots", "screen space ambient occlusion", "ambient occlusion approach", "ligand binding sites"], "article_id"=>1586093, "categories"=>["Uncategorised"], "users"=>["Manuel Wahle", "Willy Wriggers"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004516.g001", "stats"=>{"downloads"=>5, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Local_and_SSAO_rendering_of_an_atomic_structure_of_a_maltoporin_protein_PDB_ID_1AF6_/1586093", "title"=>"Local and SSAO rendering of an atomic structure of a maltoporin protein (PDB ID 1AF6).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-27 03:06:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/2381084"], "description"=>"<p>The illumination is governed by a weighted sum of unblocked light rays (red) that reach the surface point <i>p</i>, where the weights are given by the cosine of the incident angle relative to the surface normal <i>n</i><sub><i>p</i></sub>. [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004516#pcbi.1004516.ref016\" target=\"_blank\">16</a>, <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004516#pcbi.1004516.ref021\" target=\"_blank\">21</a>, <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004516#pcbi.1004516.ref022\" target=\"_blank\">22</a>].</p>", "links"=>[], "tags"=>["ambient occlusion approaches", "surface features", "Actual Sculptor screen shots", "screen space ambient occlusion", "ambient occlusion approach", "ligand binding sites"], "article_id"=>1586094, "categories"=>["Uncategorised"], "users"=>["Manuel Wahle", "Willy Wriggers"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004516.g002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_illumination_by_ambient_light_rays_red_emanating_from_a_hemisphere_937_/1586094", "title"=>"Global illumination by ambient light rays (red) emanating from a hemisphere Ω.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-27 03:06:59"}
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  • {"files"=>["https://ndownloader.figshare.com/files/2381099"], "description"=>"<p>(a) Color buffer. (b) Corresponding depth buffer contents in grayscale (black is near and white is far).</p>", "links"=>[], "tags"=>["ambient occlusion approaches", "surface features", "Actual Sculptor screen shots", "screen space ambient occlusion", "ambient occlusion approach", "ligand binding sites"], "article_id"=>1586102, "categories"=>["Uncategorised"], "users"=>["Manuel Wahle", "Willy Wriggers"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004516.g004", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_buffer_contents_/1586102", "title"=>"Illustration of buffer contents.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-27 03:06:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/2381101"], "description"=>"<p>(a-b) Point-based SSAO for (a) concavity and (b) convexity. Red marks show sample points behind the surface, green ones in front of it. In (a), most points are behind the surface, resulting in high AO. In (b), most points are in front of the surface, resulting in low AO. (c) Line-based SSAO. The green parts of the lines are in front of the surface; the red parts are hidden. Computing the ratio of visible vs. hidden parts yields an AO factor of higher granularity than what can be achieved by the point-based method.</p>", "links"=>[], "tags"=>["ambient occlusion approaches", "surface features", "Actual Sculptor screen shots", "screen space ambient occlusion", "ambient occlusion approach", "ligand binding sites"], "article_id"=>1586104, "categories"=>["Uncategorised"], "users"=>["Manuel Wahle", "Willy Wriggers"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004516.g005", "stats"=>{"downloads"=>7, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_SSAO_approaches_/1586104", "title"=>"Illustration of SSAO approaches.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-27 03:06:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/2381103"], "description"=>"<p>(a) AO with strong banding artifacts. (b) Randomized sampling. (c) Smoothing applied after the randomization.</p>", "links"=>[], "tags"=>["ambient occlusion approaches", "surface features", "Actual Sculptor screen shots", "screen space ambient occlusion", "ambient occlusion approach", "ligand binding sites"], "article_id"=>1586106, "categories"=>["Uncategorised"], "users"=>["Manuel Wahle", "Willy Wriggers"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004516.g006", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Point_Sampling_in_SSAO_/1586106", "title"=>"Point Sampling in SSAO.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-27 03:06:59"}

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