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Pipeline publication

[…] the inflated tracing result. High R values will result in large data sets of found helices at the expense of including more false positives. Consequently, precision P and recall R are interdependent, i.e. when P increases, R decreases and vice versa. As a tradeoff between precision P and recall R, we use the F1-score:(7)F1=2P·RP+R, We used Eqs. , , to assign P, R, and F1 values to single micrographs as well as to complete datasets of p62-PB1, ParM and TMV., To implement the outlined workflow, we wrote a python software program for micrograph-based helix tracing (MicHelixTrace) that is part of the SPRING software suite (). Scientific computation steps are performed by Numpy (), Scipy () and EMAN2/Sparx () libraries. The required input parameters are summarized in and listed for three different test cases. Finally, MicHelixTrace outputs either a text file containing coordinate traces in the common EMAN box format or writes out the coordinates in an sqlite3 database file spring.db for further usage inside the SPRING software suite. In addition, we added an option to generate RELION readable ∗box files. In order to compare the performance of MicHelixTrace with RELION, we used RELION 2.05 with the following input parameters: Minimum Length: 200 Å, Shrink 0.5, Angular Sampling 5°. For Tube Diameter, we used 180 Å (TMV), 100 Å (p62-PB1) and 80 Å (ParM) and Maximum Curvature was set to 0.1 (TMV), 0.4 (ParM) and 0.5 (p62-PB1), respectively. For the ParM and p62-PB1 datasets, five class averages were generated inside RELION to be used as references as suggested in the user manual. For TMV, the 2D classification algorithm converged to a maximum of three occupied classes, so three class averages were used as references. The picking threshold was optimized empirically usi […]

Pipeline specifications

Software tools FSC, SPARX, EMAN, RELION