{"id":703,"date":"2015-10-29T12:34:47","date_gmt":"2015-10-29T16:34:47","guid":{"rendered":"https:\/\/bmcresearch.utm.utoronto.ca\/sciencevislab\/?p=703"},"modified":"2015-10-30T14:28:57","modified_gmt":"2015-10-30T18:28:57","slug":"making-dna","status":"publish","type":"post","link":"https:\/\/sciencevis.ca\/index.php\/2015\/10\/29\/making-dna\/","title":{"rendered":"Making DNA"},"content":{"rendered":"[vc_row type=”in_container” scene_position=”center” text_color=”dark” text_align=”left”][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”1\/3″][vc_column_text]One of the Molecular Visualization Principles<\/a> I am currently developing is “avoiding snake motion”. This\u00a0refers to the depiction of long polymer motion, typically mRNA and DNA. To illustrate this principle, we decided to use a short linear strand of DNA.<\/p>\n

I wanted to maintain consistency of style with the other principles, so I was aiming for a specific representation that was an interesting challenge to achieve.<\/p>\n

I generated a mesh\u00a0using Molecular Maya<\/a>,\u00a0and then decided to retopologize it by hand in order to create clean topology that\u00a0was based on the atomic structure. Each nucleotide\u00a0was made from\u00a0two face loops. Edge loops were continuous along the long axis & backbone as well.[\/vc_column_text][\/vc_column][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”2\/3″]

\"DNA<\/div><\/div>[\/vc_column][\/vc_row][vc_row type=”in_container” scene_position=”center” text_color=”dark” text_align=”left”][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”2\/3″][vc_column_text][\/vc_column_text]
\"DNA<\/div><\/div>[\/vc_column][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”1\/3″][vc_column_text]Unfortunately, the short segment of DNA from the pdb (1BNA<\/a>) is not perfectly linear.\u00a0It has a twist, which I had to correct in order to duplicate and fuse the segments into a long straight mesh. I used a number of tricks, tweaks, and deformers, which resulted\u00a0in\u00a0a repeatable model, albeit one that still\u00a0had a slight twist at a longer\u00a0scale.[\/vc_column_text][\/vc_column][\/vc_row][vc_row type=”in_container” scene_position=”center” text_color=”dark” text_align=”left”][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”1\/3″][vc_column_text]I duplicated the segments and used a three-point snap to\u00a0place them correctly. Again, because of the larger scale deformation, I couldn’t just translate each segment a certain distance.\u00a0\u00a0The edge loops\u00a0that run along the backbone were very helpful in connecting these\u00a0without any guess-work.[\/vc_column_text][\/vc_column][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”2\/3″]
\"DNA<\/div><\/div>[\/vc_column][\/vc_row][vc_row type=”in_container” scene_position=”center” text_color=”dark” text_align=”left”][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”2\/3″]
\"Linear<\/div><\/div>[\/vc_column][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”1\/3″][vc_column_text]The model smooths fairly well,\u00a0isn’t too\u00a0dense,\u00a0is nicely editable, and still maintains some surface variation\u00a0rather than mathematical perfection.[\/vc_column_text][\/vc_column][\/vc_row][vc_row type=”in_container” scene_position=”center” text_color=”dark” text_align=”left”][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”1\/3″][vc_column_text]I chose a shader similar to the ones I’ve used previously in the series of molecular visualization principles<\/a>. In order to easily differentiate the ends, I wanted to create some color variation along the length of the linear DNA segment.\u00a0However, the initial color scheme\u00a0didn’t have meaning from a biological stand-point, potentially leading to confusion.[\/vc_column_text][\/vc_column][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”2\/3″]
\"CG<\/div><\/div>[\/vc_column][\/vc_row][vc_row type=”in_container” scene_position=”center” text_color=”dark” text_align=”left”][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”2\/3″]
\"DNA<\/a><\/div><\/div>[\/vc_column][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”1\/3″][vc_column_text]Ultimately, we\u00a0opted for two\u00a0color segments that cover short segments of the DNA. This still visually differentiates the ends, but could plausibly represent promoter regions or cut sites. A small amount of motion blur was applied in the final animation, hence the blurry image.[\/vc_column_text][\/vc_column][\/vc_row]\n","protected":false},"excerpt":{"rendered":"

[vc_row type=”in_container” scene_position=”center” text_color=”dark” text_align=”left”][vc_column column_padding=”no-extra-padding” column_padding_position=”all” background_color_opacity=”1″ background_hover_color_opacity=”1″ width=”1\/3″][vc_column_text]One of the Molecular Visualization Principles I am currently developing is “avoiding snake motion”. This\u00a0refers to the depiction of long polymer…<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,26],"tags":[],"class_list":{"0":"post-703","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-molecular","7":"category-process"},"_links":{"self":[{"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/posts\/703","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/comments?post=703"}],"version-history":[{"count":20,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/posts\/703\/revisions"}],"predecessor-version":[{"id":733,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/posts\/703\/revisions\/733"}],"wp:attachment":[{"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/media?parent=703"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/categories?post=703"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/sciencevis.ca\/index.php\/wp-json\/wp\/v2\/tags?post=703"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}