CYANA Macro: caliba - Revision history

Admin: /* Description */

2010-01-12T14:45:42Z

Description

← Older revision		Revision as of 16:45, 12 January 2010
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	\|backbone		\|backbone
	\|HN/HA - HN/HA, HN/HA - HA (\|''i'' - ''j''\| < 5)		\|HN/HA - HN/HA,
			HN/HA - HA (\|''i'' - ''j''\| < 5)
	\|''V'' = ''A'' / ''d''<sup>6</sup>		\|''V'' = ''A'' / ''d''<sup>6</sup>
	\|-		\|-

Admin: /* Description */

2010-01-12T14:44:49Z

Description

← Older revision		Revision as of 16:44, 12 January 2010
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	\|backbone		\|backbone
	\|HN/HA - HN/HA, HN/HA - HA (\|''i'' - ''j''\| < 5)		\|HN/HA - HN/HA, HN/HA - HA (\|''i'' - ''j''\| < 5)

	\|''V'' = ''A'' / ''d''<sup>6</sup>		\|''V'' = ''A'' / ''d''<sup>6</sup>
	\|-		\|-

Admin: /* Description */

2010-01-12T14:44:28Z

Description

← Older revision		Revision as of 16:44, 12 January 2010
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	\|backbone		\|backbone
	\|HN/HA - HN/HA,		\|HN/HA - HN/HA, HN/HA - HA (\|''i'' - ''j''\| < 5)
	HN/HA - HA (\|''i'' - ''j''\| < 5)

	\|''V'' = ''A'' / ''d''<sup>6</sup>		\|''V'' = ''A'' / ''d''<sup>6</sup>

Admin: /* Description */

2010-01-12T14:44:09Z

Description

← Older revision		Revision as of 16:44, 12 January 2010
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	Calibrates a peak list, i.e. derives upper limit distance restraints from all assigned peaks and adds them to the list of current distance restraints. Optionally, only peaks with volume larger than ''vmin'' or from a peak list with given filename (without extension) may be considered. Peaks are classified into three calibration classes:		Calibrates a peak list, i.e. derives upper limit distance restraints from all assigned peaks and adds them to the list of current distance restraints. Optionally, only peaks with volume larger than ''vmin'' or from a peak list with given filename (without extension) may be considered. Peaks are classified into three calibration classes:

	{\|		{\|border="1" cellpadding="5" cellspacing="0" style="text-align:center"
	\|Class		\|'''Class'''
	\|Peaks/restraints		\|'''Peaks/restraints'''
	\|Function		\|'''Function'''
	\|-		\|-

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	HN/HA - HA (\|''i'' - ''j''\| < 5)		HN/HA - HA (\|''i'' - ''j''\| < 5)

	\|V = A / d<sup>6</sup>		\|''V'' = ''A'' / ''d''<sup>6</sup>
	\|-		\|-

	\|sidechain		\|sidechain
	\|not "backbone" and not "methyl"		\|not "backbone" and not "methyl"
	\|V = B / d<sup>4</sup>		\|''V'' = ''B'' / ''d''<sup>4</sup>
	\|-		\|-

	\|methyl		\|methyl
	\|all involving methyl groups		\|all involving methyl groups
	\|V = C / d<sup>4</sup>		\|''V'' = ''C'' / ''d''<sup>4</sup>
	\|-		\|-
	\|}		\|}

Miki at 14:36, 12 January 2010

2010-01-12T14:36:45Z

← Older revision		Revision as of 16:36, 12 January 2010
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	== Further reading ==		== Further reading ==

	* ~~Guntert~~ et al. J. Mol. Biol. 217, 517-530 (1991).		* Güntert et al. J. Mol. Biol. 217, 517-530 (1991).
	* ~~Guntert~~ et al. J. Mol. Biol. 217, 531-540 (1991).		* Güntert et al. J. Mol. Biol. 217, 531-540 (1991).
	* Mumenthaler et al. J. Biomol. NMR. 10, 351-362 (1997).		* Mumenthaler et al. J. Biomol. NMR. 10, 351-362 (1997).

Miki: /* Description */

2010-01-12T14:27:33Z

Description

← Older revision		Revision as of 16:27, 12 January 2010
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	Optionally, the resulting distance restraints may be given a relative ''weight'', and a logarithmic plot of volumes versus corresponding minimal distances in the selected structures can be written.		Optionally, the resulting distance restraints may be given a relative ''weight'', and a logarithmic plot of volumes versus corresponding minimal distances in the selected structures can be written.

			== Further reading ==

			* Guntert et al. J. Mol. Biol. 217, 517-530 (1991).
			* Guntert et al. J. Mol. Biol. 217, 531-540 (1991).
			* Mumenthaler et al. J. Biomol. NMR. 10, 351-362 (1997).

Miki: /* Description */

2010-01-12T14:25:10Z

Description

← Older revision		Revision as of 16:25, 12 January 2010
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	Calibrates a peak list, i.e. derives upper limit distance restraints from all assigned peaks and adds them to the list of current distance restraints. Optionally, only peaks with volume larger than ''vmin'' or from a peak list with given filename (without extension) may be considered. Peaks are classified into three calibration classes:		Calibrates a peak list, i.e. derives upper limit distance restraints from all assigned peaks and adds them to the list of current distance restraints. Optionally, only peaks with volume larger than ''vmin'' or from a peak list with given filename (without extension) may be considered. Peaks are classified into three calibration classes:

	{\|		{\|
	\|Class		\|Class
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	\|V = B / d<sup>4</sup>		\|V = B / d<sup>4</sup>
	\|-		\|-

	\|}


	\|methyl		\|methyl
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	\|V = C / d<sup>4</sup>		\|V = C / d<sup>4</sup>
	\|-		\|-
			\|}

	The parameters ''A'', ''B'', ''C'' are either given by the user (A = ''bb'', B = ''sc'' and C = ''methyl''), or calculated automatically using the function [[CYANA Functions: calscale\|'''calscale''']] to determine A by assuming an average distance ''avedis'' for the restraints in the class “backbone” and setting B = A / up1_values(1) and C = B / 3.		The parameters ''A'', ''B'', ''C'' are either given by the user (A = ''bb'', B = ''sc'' and C = ''methyl''), or calculated automatically using the function [[CYANA Functions: calscale\|'''calscale''']] to determine A by assuming an average distance ''avedis'' for the restraints in the class “backbone” and setting B = A / up1_values(1) and C = B / 3.

	Optionally, the resulting distance restraints may be given a relative ''weight'', and a logarithmic plot of volumes versus corresponding minimal distances in the selected structures can be written.		Optionally, the resulting distance restraints may be given a relative ''weight'', and a logarithmic plot of volumes versus corresponding minimal distances in the selected structures can be written.

Miki: /* Description */

2010-01-12T14:24:41Z

Description

← Older revision		Revision as of 16:24, 12 January 2010
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	\|V = B / d<sup>4</sup>		\|V = B / d<sup>4</sup>
	\|-		\|-

			\|}


	\|methyl		\|methyl

Miki: /* Description */

2010-01-12T14:23:58Z

Description

← Older revision		Revision as of 16:23, 12 January 2010
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	\|-		\|-

			The parameters ''A'', ''B'', ''C'' are either given by the user (A = ''bb'', B = ''sc'' and C = ''methyl''), or calculated automatically using the function [[CYANA Functions: calscale\|'''calscale''']] to determine A by assuming an average distance ''avedis'' for the restraints in the class “backbone” and setting B = A / up1_values(1) and C = B / 3.

			Optionally, the resulting distance restraints may be given a relative ''weight'', and a logarithmic plot of volumes versus corresponding minimal distances in the selected structures can be written.

	* The “backbone” class includes all distance restraints between the backbone amide and α protons that are less than five residues apart from each other. A relationship ''V = A / u<sup>6</sup>'' between the peak volume ''V'' and the upper distance bound ''u'' is assumed.
	* The “sidechain” class includes all distance restraints that do not belong to one of the other classes. A relationship ''V = B / u<sup>4</sup>'' between the peak volume ''V'' and the upper distance bound ''u'' is assumed.
	* The “methyl” class includes all distance restraints that involve a methyl group. A relationship ''V = C / u<sup>4</sup>'' between the peak volume ''V'' and the upper distance bound ''u'' is assumed.

	~~The parameters ''A'', ''B''~~, ~~''C'' are either given by~~ the ~~user as ''A = bb'', ''B = sc'' and ''C = methyl'', or calculated automatically as follows: The function [[CYANA Functions: calscale\|'''calscale''']] is used to calculate ''A'' by assuming an average~~ distance ~~''avedis'' for all~~ restraints ~~in the class “backbone”. By default, the scalar ''B'' is set to ''B = A / d<sup>2</sup><sub>min</sub>'' , where ''d<sub>min</sub>'' is the minimal upper distance bound~~ given ~~by the system variable [[CYANA Variables: upl_values\|~~'''~~upl_values~~'~~'']]~~, and ~~''C'' is set to ''B / 3'' (Mumenthaler et al., 1997). Optionally,~~ a logarithmic plot of volumes versus corresponding minimal distances in the selected structures can be ~~created~~.

Miki: /* Description */

2010-01-12T14:16:20Z

Description

← Older revision		Revision as of 16:16, 12 January 2010
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	\|-		\|-

			\|sidechain
			\|not "backbone" and not "methyl"
			\|V = B / d<sup>4</sup>
			\|-

			\|methyl
			\|all involving methyl groups
			\|V = C / d<sup>4</sup>
			\|-