Fig. 3

BpForms and BcForms can generate molecular and genomic visualizations of macromolecules. BpForms can generate molecular visualizations of residues such as phosphoserine (a), crosslinks such as an isoaspartyl glycine isopeptide bond (b), and polymers such as the tripeptide ACD (c). The blue and green letters in a indicate the atoms which can bond with preceding and following residues; the light blue and green letters indicate the atoms which are displaced by the formation of these bonds. The blue and green elements in b indicate the individual residues involved in the crosslink; the red line indicates the covalent bond that crosslinks the residues. The green elements in c indicate the first and third residues in the peptide, the blue elements indicate the second residue, and the red lines indicate the covalent bonds between the residues. BpForms and BcForms can also generate sequence-based visualizations of polymers and complexes such as the pupylation of chaperonin GroS (d). The left and right tracks indicate the canonical residues of GroS and Pup, respectively. The gray letters indicate the residues which are removed post-translationally. The horizontal red letters indicate the residues which are post-translationally modified. The rotated red letters indicate the type of each post-translational modification. The green line indicates the residues which are post-translationally crosslinked