CYANA Command: write upl - Revision history

Masayo: /* Description */

2010-01-12T10:11:43Z

Description

← Older revision		Revision as of 12:11, 12 January 2010
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	== Description ==		== Description ==

	Writes ~~a file with the currently selected~~ upper ~~distance limits in the standard [[~~distance restraint file~~]] format of~~ the ~~program CYANA, or optionally in XPLOR format~~.		Writes an upper limit distance restraint file. Optionally, the output may be appended to an existing file.

	==== Ambiguous distance restraints ====		==== Ambiguous distance restraints ====

Masayo: /* Parameters */

2010-01-12T10:09:29Z

Parameters

← Older revision		Revision as of 12:09, 12 January 2010
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	== Parameters ==		== Parameters ==

	; file=''filename''.upl		; file=''filename''.upl:(required)
	:(~~required~~) ~~The name of the output upper distance limit file. The~~ default ~~filename extension ".upl" is used unless a filename extension is given explicitly.~~		;list=''integer'':(default: 1)
	; sorted		;nmrstar=''integer'':(default: 2)
	: Option to sort the distance restraints by the first and second atom. By default, the distance restraints are written in the order in which they are stored in the program, e.g. the order in which they have been read from an input file.		;details
	; swapped		;multiple
	~~: Option to output restraints that involve diastereotopic hydrogens or methyl groups after optimal swapping of the stereopartners for minimal target function value.~~		;sorted
	; xplor		;swapped
	~~: Option to output the file in the format of the program XPLOR instead of the standard [[distance restraint file]] format of the program CYANA.~~		;xplor
	; nocomments		;nocomments
	~~: Option to suppress the output of comments such as the number of the peak from which the restraint originated.~~		;append
	; append
	~~: Option to append the output to the given file. By default, an already existing output file is overwritten.~~

	== Description ==		== Description ==

Guentert: /* Ambiguous distance restraints */

2009-02-18T22:40:54Z

Ambiguous distance restraints

← Older revision		Revision as of 00:40, 19 February 2009
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	Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition		Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition

	~~<center>~~<math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.~~</center>~~		:<math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.

	''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>.		''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>.

Guentert: /* Ambiguous distance restraints */

2009-02-05T22:58:57Z

Ambiguous distance restraints

← Older revision		Revision as of 00:58, 6 February 2009
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	<center><math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.</center>		<center><math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.</center>

	''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.		''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>.

			Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.

	==== Shorthand form ====		==== Shorthand form ====

Guentert: /* Ambiguous distance restraints */

2009-02-05T22:58:35Z

Ambiguous distance restraints

← Older revision		Revision as of 00:58, 6 February 2009
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	Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition		Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition

	<center><math>~~\displaystyle~~ d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.</center>		<center><math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.</center>

	''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.		''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.

Guentert: /* Ambiguous distance restraints */

2009-02-05T22:56:40Z

Ambiguous distance restraints

← Older revision		Revision as of 00:56, 6 February 2009
Line 24:		Line 24:
	Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition		Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition

	<center><math>\~~displayequation{~~d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b}</math>.</center>		<center><math>\displaystyle d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.</center>

	''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.		''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.

Guentert: /* Ambiguous distance restraints */

2009-02-05T22:56:02Z

Ambiguous distance restraints

← Older revision		Revision as of 00:56, 6 February 2009
Line 24:		Line 24:
	Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition		Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition

	<center><math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.</center>		<center><math>\displayequation{d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b}</math>.</center>

	''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.		''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.

Guentert: /* Ambiguous distance restraints */

2009-02-05T22:55:26Z

Ambiguous distance restraints

← Older revision		Revision as of 00:55, 6 February 2009
Line 26:		Line 26:
	<center><math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.</center>		<center><math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.</center>

	''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled If at least one of the assignments corresponds to a distance		''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances.

	==== Shorthand form ====		==== Shorthand form ====

Guentert: /* Ambiguous distance restraints */

2009-02-05T22:53:49Z

Ambiguous distance restraints

← Older revision		Revision as of 00:53, 6 February 2009
Line 26:		Line 26:
	<center><math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.</center>		<center><math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>.</center>

	''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>.		''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled If at least one of the assignments corresponds to a distance

	==== Shorthand form ====		==== Shorthand form ====

Guentert: /* Description */

2009-02-05T22:47:59Z

Description

← Older revision		Revision as of 00:47, 6 February 2009
Line 20:		Line 20:
	Writes a file with the currently selected upper distance limits in the standard [[distance restraint file]] format of the program CYANA, or optionally in XPLOR format.		Writes a file with the currently selected upper distance limits in the standard [[distance restraint file]] format of the program CYANA, or optionally in XPLOR format.

	=== Ambiguous distance restraints ===		==== Ambiguous distance restraints ====

	Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition		Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition
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	''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>.		''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>.

	=== Shorthand form ===		==== Shorthand form ====

	Instead of the command		Instead of the command