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Moloc: Molecular Modelling on UNIX Workstations: 17 X-ray and NMR Utility [xnr]

X-ray and NMR Utility [xnr]

A collection of utilities, useful for structure evaluation in connection with structure determination by X-ray or NMR methods.

NOE Violation Display

Violation of distance constraints can be examined here. First a file has to be read in with a list of constraints. Currently the DIANA format is supported. The violations are indicated by dashed lines of a color indicative of the amount of violation. The color code is given on the menu bar. The threshold value can be adjusted by the user. Depending on its value different things will be displayed.

H-bond Pattern Search [hbpt]

For a set of molecules of identical topology a list of possible patterns of hydrogen bonds is calculated. After specification of the participant donor-acceptors (donac), weights for all possible donor-acceptor pairs of are calculated. A weight is determined by the energy of the corresponding H-bond within the MAB force field. If only a fraction of all donac's is specified one has to be aware of the fact that H-bonds to non-specified donac's may exist. As a consequence the true number of donor or acceptor counts attributable to a donac may be lower than assumed in the evaluation!

SS-Bridge Pattern Evaluation [ssb]

For a set of proteins of identical topology a list of possible patterns of disulfide bridges is calculated. In a first step weights for all possible pairs of cysteines are calculated. The weight is determined by the distance of the corresponding beta carbons or sulfurs. It is highest for the ideal distance. The width of the weight function determines the weights for other distances. Several parameters that determine the details of the evaluation can be set by the user.

Residue-wise Coloring of Sets on Proteins [ptcl]

This utility allows to display sets of all-atom protein structures selectively by specifying which residues should appear in which color and which portions of the backbone should be displayed. The backbones are drawn in the color of the entries, while the residues can be assigned to color- specific sets. Alternatively, the specified residues can be made to assume the entry color. As a first step a structure has to be picked, whereupon the associated Calf structure is generated. It becomes visible whenever the user chooses to specify a color-specific or the backbone set. When leaving the menu all specified sets are lost.

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