Guentert at 15:42, 9 February 2009

2009-02-09T15:42:29Z

← Older revision		Revision as of 17:42, 9 February 2009
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	:<math>V = \sum_{c=u,l,v} w_c \sum_{(\alpha,\beta)\in I_c} w_{\alpha\beta}^c (d_{\alpha\beta} - b_{\alpha\beta})^2 + w_a \sum_{i\in I_a} w_i \left[1 - \frac{1}{2}\left(\frac{\Delta_i}{\Gamma_i}\right)^2\right]\Delta_i^2</math>		:<math>V = \sum_{c=u,l,v} w_c \sum_{(\alpha,\beta)\in I_c} w_{\alpha\beta}^c (d_{\alpha\beta} - b_{\alpha\beta})^2 + w_a \sum_{i\in I_a} w_i \left[1 - \frac{1}{2}\left(\frac{\Delta_i}{\Gamma_i}\right)^2\right]\Delta_i^2</math>

	Upper and lower bounds, ''b<sub>αβ</sub>'', on distances ''d<sub>αβ</sub>'' between two atoms ''α'' and ''β'', and restraints on individual torsion angles ''θ<sub>i</sub>'' in the form of allowed intervals <math>[\theta_i^\min,\theta_i^\max]</math> are considered. ''I<sub>u</sub>'', ''I<sub>l</sub>'' and ''I<sub>v</sub>'' are the sets of atom pairs (''α'',''β'') with violated upper, lower or van der Waals distance bounds, respectively, and ''I<sub>a</sub>'' is the set of restrained torsion angles. ''w<sub>u</sub>'', ''w<sub>l</sub>'', ''w<sub>v</sub>'' and ''w<sub>a</sub>'' are overall weighting factors for the different types of restraints, and <math>w_{\alpha\beta}^c</math> and ''w<sub>i</sub>'' are relative weighting factors for individual restraints. The half-width of the forbidden range of torsion angle values is denoted by <math>\Gamma_i = \pi - (\theta_i^\max - \theta_i^\min)/2</math>, and ''Δ<sub>i</sub>'' is the size of the torsion angle restraint violation.		Upper and lower bounds, ''b<sub>αβ</sub>'', on distances ''d<sub>αβ</sub>'' between two atoms ''α'' and ''β'', and restraints on individual torsion angles ''θ<sub>i</sub>'' in the form of allowed intervals <math>\scriptstyle [\theta_i^\min,\theta_i^\max]</math> are considered. ''I<sub>u</sub>'', ''I<sub>l</sub>'' and ''I<sub>v</sub>'' are the sets of atom pairs (''α'',''β'') with violated upper, lower or van der Waals distance bounds, respectively, and ''I<sub>a</sub>'' is the set of restrained torsion angles. ''w<sub>u</sub>'', ''w<sub>l</sub>'', ''w<sub>v</sub>'' and ''w<sub>a</sub>'' are overall weighting factors for the different types of restraints, and <math>\scriptstyle w_{\alpha\beta}^c</math> and ''w<sub>i</sub>'' are relative weighting factors for individual restraints. The half-width of the forbidden range of torsion angle values is denoted by <math>\scriptstyle \Gamma_i = \pi - (\theta_i^\max - \theta_i^\min)/2</math>, and ''Δ<sub>i</sub>'' is the size of the torsion angle restraint violation.

	The target function may include additional terms for restraints on vicinal scalar coupling constants, residual dipolar couplings, and pseudocontact shifts, as well as identity and symmetry restraints for symmetric multimers. Alternatives to the simple square potential for violated distance restraints have also been implemented.		The target function may include additional terms for restraints on vicinal scalar coupling constants, residual dipolar couplings, and pseudocontact shifts, as well as identity and symmetry restraints for symmetric multimers. Alternatives to the simple square potential for violated distance restraints have also been implemented.

84.178.117.174: New page: The CYANA target function (Güntert et al., 1991; Güntert et al., 1997) is defined such that it is zero if and only if all experimental distance restraints and torsion angle restraints ar...

2009-02-08T16:37:10Z

New page: The CYANA target function (Güntert et al., 1991; Güntert et al., 1997) is defined such that it is zero if and only if all experimental distance restraints and torsion angle restraints ar...

New page

The CYANA target function (Güntert et al., 1991; Güntert et al., 1997) is defined such that it is zero if and only if all experimental distance restraints and torsion angle restraints are fulfilled and all non-bonded atom pairs satisfy a check for the absence of steric overlap. A conformation that satisfies the restraints more closely than another one will lead to a lower target function value. The CYANA target function for distance restraints and torsion angle restraints is defined by

:<math>V = \sum_{c=u,l,v} w_c \sum_{(\alpha,\beta)\in I_c} w_{\alpha\beta}^c (d_{\alpha\beta} - b_{\alpha\beta})^2 + w_a \sum_{i\in I_a} w_i \left[1 - \frac{1}{2}\left(\frac{\Delta_i}{\Gamma_i}\right)^2\right]\Delta_i^2</math>

Upper and lower bounds, ''bαβ'', on distances ''dαβ'' between two atoms ''α'' and ''β'', and restraints on individual torsion angles ''θi'' in the form of allowed intervals <math>[\theta_i^\min,\theta_i^\max]</math> are considered. ''Iu'', ''Il'' and ''Iv'' are the sets of atom pairs (''α'',''β'') with violated upper, lower or van der Waals distance bounds, respectively, and ''Ia'' is the set of restrained torsion angles. ''wu'', ''wl'', ''wv'' and ''wa'' are overall weighting factors for the different types of restraints, and <math>w_{\alpha\beta}^c</math> and ''wi'' are relative weighting factors for individual restraints. The half-width of the forbidden range of torsion angle values is denoted by <math>\Gamma_i = \pi - (\theta_i^\max - \theta_i^\min)/2</math>, and ''Δi'' is the size of the torsion angle restraint violation.

The target function may include additional terms for restraints on vicinal scalar coupling constants, residual dipolar couplings, and pseudocontact shifts, as well as identity and symmetry restraints for symmetric multimers. Alternatives to the simple square potential for violated distance restraints have also been implemented.

Target function - Revision history

Guentert at 15:42, 9 February 2009

84.178.117.174: New page: The CYANA target function (Güntert et al., 1991; Güntert et al., 1997) is defined such that it is zero if and only if all experimental distance restraints and torsion angle restraints ar...