{"id":865,"date":"2016-03-24T10:57:17","date_gmt":"2016-03-24T14:57:17","guid":{"rendered":"https:\/\/research.cbc.osu.edu\/foster.281\/?page_id=865"},"modified":"2016-03-24T10:57:17","modified_gmt":"2016-03-24T14:57:17","slug":"figure-prep","status":"publish","type":"page","link":"https:\/\/research.cbc.osu.edu\/foster.281\/figure-prep\/","title":{"rendered":"Figure Preparation in the Foster Lab"},"content":{"rendered":"<p>Preparing scientific figures for manuscripts, presentations and grant applications<\/p>\n<h1 class=\"western\">Glossary<\/h1>\n<ul>\n<li>Vector format: a graphics format in which images are produced via commands (draw line from x1,y1 to x2,y2). This format can be scaled infinitely with no loss of resolution.<\/li>\n<li>Raster or bitmat format: Images composed of a grid of pixels in which each pixel has a different color. The resolution of the image is set by the number of pixels (e.g., 150 dpi)<\/li>\n<\/ul>\n<h1>Preferred Software<\/h1>\n<ul>\n<li>Graphics anotating: Powerpoint, Illustrator\n<ul>\n<li>Alternatives: LibreOffice Presenter, Keynote, Inkscape<\/li>\n<\/ul>\n<\/li>\n<li>Image manipulation: Graphic Converter (Mac), GIMP (LINUX), Photoshop<\/li>\n<\/ul>\n<h1 class=\"western\">General rules of thumb<\/h1>\n<ul>\n<li>Use Helvetica or Arial for figure text<\/li>\n<li>Use sufficiently large text so that it can be clearly read when printed at the intended size<\/li>\n<li>Do not allow figure elements to clash\/overlap (annotations, lines, images, legends)<\/li>\n<li>When possible, prepare figures using vector format, not raster\/bitmap<\/li>\n<li>Figures should be prepared separately, including annotations\/labels, then embedded intact into a text document \u2013 do not try to edit a figure within a word processing program!<\/li>\n<li>Use black and white unless color is necessary to illustrate a point<\/li>\n<\/ul>\n<h1 class=\"western\">Preparing nD NMR spectra<\/h1>\n<ul>\n<li>Be sure to simplify the figure to focus the reader&#8217;s attention to the spectral features of interest \u2013 do not expect a reader to interpret the spectrum on their own. This usually means zooming-in on a region of interest, at the expense of the full spectrum<\/li>\n<li>If a full spectrum is to be shown, minimize blank space, and ensure that peak labels do not overlap<\/li>\n<li>From the NMR program, output the spectrum in scalable vector format (usually PS or PDF)<\/li>\n<li>Import the file into software that can edit vector graphics files (Adobe Illustrator, Inkscape)<\/li>\n<li>Add\/manipulate text and annotations in vector format \u2013 change fonts as required<\/li>\n<li>Crop\/expand figures as needed so to minimize blank space around the figure<\/li>\n<li>Reduce the number of contours and\/or inter-contour spacing to minimize file size<\/li>\n<li>Save annotated spectra in both vector and image formats. The image files should have a minimum resolution of 150-300 dpi for items to be printed.<\/li>\n<\/ul>\n<h1 class=\"western\">Preparing images of structures (mostly via PyMOL)<\/h1>\n<ul>\n<li>Use PyMOL&#8217;s ray-trace mode<\/li>\n<li>in ribbon diagrams, when showing sidechains via sticks, hide backbone atoms (proteins: n, o and c; NA: o1p, o2p, p), unless they are needed to illustrate a point<\/li>\n<li>Minimize blank space<\/li>\n<li>Add annotations in vector format (Powerpoint or Libreoffice Presenter preferred; Keynote, Illustrator or Inkscape OK)<\/li>\n<li>Generate high-resolution bitmap image (png, jpg or tiff; 300+ dpi).<\/li>\n<\/ul>\n<h1 class=\"western\">Importing into documents<\/h1>\n<ul>\n<li>Copy-pasting of images into documents often has unpredictable results.<\/li>\n<li>DO import\/insert figures into the document<\/li>\n<li>Do NOT draw line borders around embedded images<\/li>\n<\/ul>\n<h1 class=\"western\">Figure legends\/captions<\/h1>\n<ul>\n<li>Figure legends should describe the figure and the point to be made<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Preparing scientific figures for manuscripts, presentations and grant applications Glossary Vector format: a graphics format in which images are produced via commands (draw line from x1,y1 to x2,y2). This format can be scaled infinitely with no loss of resolution. Raster<\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"jetpack_post_was_ever_published":false,"footnotes":""},"class_list":["post-865","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/P7sxod-dX","jetpack-related-posts":[{"id":1698,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/foster-group-guide\/","url_meta":{"origin":865,"position":0},"title":"Foster Group Guide","author":"Mark Foster","date":"March 26, 2021","format":false,"excerpt":"Foster Group Guide https:\/\/research.cbc.osu.edu\/foster.281\/foster-group-guide\/ Expectations A Ph.D. scientist is expected to be the world expert in the area of his\/her research. Consequently, a graduate education must produce a scientist capable of (1) thinking independently, (2) identifying a research problem (i.e., a testable hypothesis), (3) devising the means with which to\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1869,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/foster-group-guide-2\/","url_meta":{"origin":865,"position":1},"title":"Foster Group Guide","author":"Mark Foster","date":"April 18, 2023","format":false,"excerpt":"Foster Group Guide https:\/\/research.cbc.osu.edu\/foster.281\/foster-group-guide\/ Expectations A Ph.D. scientist is expected to be the world expert in the area of his\/her research. Consequently, a graduate education must produce a scientist capable of (1) thinking independently, (2) identifying a research problem (i.e., a testable hypothesis), (3) devising the means with which to\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":632,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/research-areas\/protein-nucleic-acid-interactions\/","url_meta":{"origin":865,"position":2},"title":"Protein-Nucleic Acid Interactions","author":"Mark Foster","date":"January 17, 2016","format":false,"excerpt":"Protein-Nucleic Acid Interactions TRAP\u00a0 \u2666 \u00a0RNase P \u00a0\u2666\u00a0 Loz1 \u2666 \u00a0tRNA Editing\u00a0 \u2666\u00a0 Tyrosine Recombinases TRAP The ring-forming oligomeric Bacillus trp RNA binding attenuation protein (TRAP), defines a paradigm for gene regulation by ligand-mediated alteration of the structure of non-coding RNA, and for mechanisms of both homotropic and heterotropic allostery.\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/research.cbc.osu.edu\/foster.281\/wp-content\/uploads\/2016\/01\/pxpa-shifting-194x300.png?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":693,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/links\/literature-presentations\/","url_meta":{"origin":865,"position":3},"title":"Literature Presentations","author":"Mark Foster","date":"February 5, 2016","format":false,"excerpt":"Literature Presentations in the Foster Lab Objectives Improve our breadth of knowledge of research in areas related to ours Increase the breadth of our understanding of problems, techniques and concepts related to our research Learn to read research literature critically, and to identify important knowledge or methodological gaps Practice our\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"_links":{"self":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/pages\/865","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/comments?post=865"}],"version-history":[{"count":2,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/pages\/865\/revisions"}],"predecessor-version":[{"id":867,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/pages\/865\/revisions\/867"}],"wp:attachment":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/media?parent=865"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}