Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Image analysis

DO Davi R. Ortega
WY Wen Yang
PS Poorna Subramanian
PM Petra Mann
AK Andreas Kjær
SC Songye Chen
KW Kylie J. Watts
SP Sahand Pirbadian
DC David A. Collins
RK Romain Kooger
MK Marina G. Kalyuzhnaya
SR Simon Ringgaard
AB Ariane Briegel
GJ Grant J. Jensen
request Request a Protocol
ask Ask a question
Favorite

CTF correction, frame alignment and SIRT reconstruction was done using the IMOD software package40,41. Sub-tomogram averaging was carried out with the Dynamo software package42,43. F7 arrays were modeled as patches of surfaces in individual tomograms, and then particles containing IM and baseplate were cropped out based on the geometry of the surface model. Information about the number of cells, particles and pixel sizes are summarized in Supplementary Table 3. Particles were aligned first based on the IM and baseplate density, and then subsequently aligned with in-plane rotations and shifts. 2D tomoslices of the averages represent the top view and the side view of the repeating unit of the F7 arrays. A side view image was used for comparison to the receptor homology models.

Copyright and License information: The Author(s) ©2020
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

post Post a Question
0 Q&A