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Figure 4
Defining restraints for the covalent linkage Lys–PLP using JLigand. Snapshots show the state of the JLigand interface after the following user actions: (a) loading monomers LYS and PLP from the restraint library, (b) removing O4A from PLP, (c) connecting C4A (PLP) with NZ (LYS) and defining the bond order and (d) regularization. The Save As Link menu has to be used to generate (e) an additional library file containing the following five data blocks: list of modifications, list of links, modifications LYSmod1 and PLPmod1 to be applied to LYS and PLP, respectively, and link LYS–PLP. The file header, tables of restraints for LYSmod1 and all the tables for PLPmod1 are omitted, as indicated by lines filled by tildes. H atoms are dealt with automatically. It is also possible to visualize them and handle them explicitly.

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
Volume 68| Part 4| April 2012| Pages 431-440
https://doi.org/10.1107/S090744491200251X
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