Hi Dmitry, The main answer is to use your own scientific judgment, as I'm not aware of specific guidelines or rules, and we do not "prescribe" a certain behavior. However, it's worth mentioning that many very good papers mention using Chimera "hide dust" (same feature as in ChimeraX) ... here are a couple of recent open-access examples: CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. Brilot AF, Lyon AS, Zelter A, Viswanath S, Maxwell A, MacCoss MJ, Muller EG, Sali A, Davis TN, Agard DA. Elife. 2021 May 5;10:e65168. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099430/> Cryo-EM structure of enteric adenovirus HAdV-F41 highlights structural variations among human adenoviruses. Perez-Illana M, Martinez M, Condezo GN, Hernando-Perez M, Mangroo C, Brown M, Marabini R, San Martín C. Sci Adv. 2021 Feb 24;7(9):eabd9421. <https://advances.sciencemag.org/content/7/9/eabd9421> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 20, 2021, at 3:13 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear colleagues, I would like to ask you for the common practice in showing the threshold of the 3D map and usage of the "hide dust tool”.

Am I allowed to use the “hide dust tool” when making the figures for the paper? And if yes, if/how shall I specify that in the description to the figure?

Thank you Sincerely, Dmitry