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Structural biologists, lets mind our colors

Saladi, Shyam M. and Maggiolo, Ailiena O. and Radford, Kate and Clemons, William M., Jr. (2020) Structural biologists, lets mind our colors. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200925-104733901

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Abstract

In structural biology, most figures of macromolecules are aimed at those well-versed in structure, requiring prior familiarity with scales and commonly used color schemes. Yet, as structural biology becomes democratized with the increasing pace of structure determination, the accessibility of structural data is paramount. Here, we identify three keys, and have written accompanying software plugins, for structural biologists to create figures truer to the hard-won data and clearer across different modes of color vision and to non-expert readers. Use perceptually uniform colormaps Consider readers with different modes of color vision Be explicit about scales and color usage


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.09.22.308593DOIDiscussion Paper
https://github.com/smsaladi/pymol_viridisRelated ItemData/Code
https://github.com/smsaladi/chimerax_viridisRelated ItemData/Code
https://github.com/smsaladi/vmd_viridisRelated ItemData/Code
https://github.com/smsaladi/structure_scalesRelated ItemData/Code
ORCID:
AuthorORCID
Saladi, Shyam M.0000-0001-9701-3059
Maggiolo, Ailiena O.0000-0003-1707-5060
Radford, Kate0000-0001-8484-7580
Clemons, William M., Jr.0000-0002-0021-889X
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. We thank members of the Clemons and Rees labs for discussion and S. Petrovic for comments on the manuscript. This work was supported by the National Institutes of Health (NIH) grants GM105385 and GM097572 (to WMC) and a National Science Foundation Graduate Research fellowship Grant 1144469 (to SMS). Software availability. Patches to make Viridis and accompanying colormaps easily accessible in PyMOL, ChimeraX, and VMD can be found here: https://github.com/smsaladi/pymol_viridis, https://github.com/smsaladi/chimerax_viridis, https://github.com/smsaladi/vmd_viridis. A guide for creating a scalebar across various visualization programs can be found here: https://github.com/smsaladi/structure_scales. All code is made available under the open-source MIT License and will be deposited in the CaltechDATA institutional repository. The authors have declared no competing interest.
Funders:
Funding AgencyGrant Number
NIHGM105385
NIHGM097572
NSF Graduate Research FellowshipDGE-1144469
Subject Keywords:data visualization, accessibility, perceptual uniformity, visual artefact, colormap, color palette, color vision deficiency, macromolecular structure
Record Number:CaltechAUTHORS:20200925-104733901
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200925-104733901
Official Citation:Structural biologists, let’s mind our colors Shyam M. Saladi, Ailiena O. Maggiolo, Kate Radford, William M. Clemons Jr. bioRxiv 2020.09.22.308593; doi: https://doi.org/10.1101/2020.09.22.308593
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:105547
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:25 Sep 2020 20:28
Last Modified:06 Nov 2020 19:52

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