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Figure 1
FLEXR-MSA workflow for comparison of alternative side-chain conformations in electron-density maps across related, sequence-diverse proteins. (1) FLEXR-MSA reads in the CSV output file with the σ values from Ringer (Lang et al., 2010BB35), (2) extracts the amino-acid sequence from the Ringer output, formats the sequences into FASTA, and (3) performs a multiple sequence alignment (MSA) using MUSCLE (Edgar, 2004BB15). (4) Residues in each sequence are re-indexed according to their position in the alignment. (5) σ values at each position in the alignment for each sequence are extracted. (6) σ values are plotted as classical Ringer plots where the plot title corresponds to the MSA index and the residue numbers are shown in the legend. A PDB file is also generated that contains median Pearson CC values that can be visualized in PyMOL.

IUCrJ
Volume 12| Part 2| March 2025| Pages 245-254
ISSN: 2052-2525
https://doi.org/10.1107/S2052252525001332