NOE Calibration Using CYANA - Revision history

Jma at 21:53, 6 January 2010

2010-01-06T21:53:43Z

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Jma at 21:53, 6 January 2010

2010-01-06T21:53:03Z

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	~~-- AlexEletski - 12 Jun 2007~~

	~~-- Edited by JimAramini - Nov 2009~~

Jma at 23:49, 13 November 2009

2009-11-13T23:49:28Z

Jma at 23:48, 13 November 2009

2009-11-13T23:48:40Z

← Older revision		Revision as of 23:48, 13 November 2009
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	=== Initial NOE Calibration ===		=== Initial NOE Calibration ===

	After simulating and filtering one typically has three initial NOESY peaklists, for example, <~~code~~>n.peaks</~~code~~>, <~~code~~>ali.peaks</~~code~~>, and <~~code~~>aro.peaks</~~code~~>. The assigned peaks are intra-residue and short-range within secondary structure elements. Initial calibration is needed to verify these assignments for consistency with molecular geometry and, if possible, to derive stereospecific assignments with HABAS in CYANA. If your SequenceList and AtomList were generated with XEASY, you will need to convert them to the format of CYANA 2.1 (see the <~~code~~>~/demo/details/MigrateFromDyanaCyana1.cya</~~code~~> example script). SequenceList and AtomList from CARA are already compatible.		After simulating and filtering one typically has three initial NOESY peaklists, for example, <tt>n.peaks</tt>, <tt>ali.peaks</tt>, and <tt>aro.peaks</tt>. The assigned peaks are intra-residue and short-range within secondary structure elements. Initial calibration is needed to verify these assignments for consistency with molecular geometry and, if possible, to derive stereospecific assignments with HABAS in CYANA. If your SequenceList and AtomList were generated with XEASY, you will need to convert them to the format of CYANA 2.1 (see the <tt>~/demo/details/MigrateFromDyanaCyana1.cya</tt> example script). SequenceList and AtomList from CARA are already compatible.

	Amide, aliphatic and aromatic protons tend to have different relaxation properties in a simultaneous 3D 15N-, 13C-resolved NOESY.  NOESY spectra acquired separately may have varying acquisition times. Therefore, it is recommended to run <~~code~~>caliba</~~code~~> separately for each peaklist.		Amide, aliphatic and aromatic protons tend to have different relaxation properties in a simultaneous 3D 15N-, 13C-resolved NOESY.  NOESY spectra acquired separately may have varying acquisition times. Therefore, it is recommended to run <tt>caliba</tt> separately for each peaklist.

	Here is a sample [[Media:Run_caliba.cya\|run_caliba.cya]] script for running <~~code~~>caliba</~~code~~> on all three peaklists:		Here is a sample [[Media:Run_caliba.cya\|run_caliba.cya]] script for running <tt>caliba</tt> on all three peaklists:
	<pre>protocol:=caliba.log		<pre>protocol:=caliba.log
	read prot $name		read prot $name
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	write upl short.upl		write upl short.upl
	protocol:=</pre>		protocol:=</pre>
	Note that you need to convert volumes to absolute values before calling <~~code~~>caliba</~~code~~>, otherwise negative intensities will be misinterpreted.		Note that you need to convert volumes to absolute values before calling <tt>caliba</tt>, otherwise negative intensities will be misinterpreted.

	Macro <~~code~~>caliba</~~code~~> should work fine for <~~code~~>n.peaks</~~code~~> and <~~code~~>ali.peaks</~~code~~> with default parameters. Aromatic peaklist <~~code~~>aro.peaks</~~code~~> requires special treatment because it does not have any peaks of the backbone class. '''For aromatic peaklists <~~code~~>caliba</~~code~~> should be run either with a single <~~code~~>bb</~~code~~> parameter or with both <~~code~~>bb</~~code~~> and <~~code~~>sc</~~code~~> parameters. Calling it without <~~code~~>bb</~~code~~> parameter will cause an error.'''		Macro <tt>caliba</tt> should work fine for <tt>n.peaks</tt> and <tt>ali.peaks</tt> with default parameters. Aromatic peaklist <tt>aro.peaks</tt> requires special treatment because it does not have any peaks of the backbone class. '''For aromatic peaklists <tt>caliba</tt> should be run either with a single <tt>bb</tt> parameter or with both <tt>bb</tt> and <tt>sc</tt> parameters. Calling it without <tt>bb</tt> parameter will cause an error.'''

	The <~~code~~>sc</~~code~~> and <~~code~~>bb</~~code~~> parameters for <~~code~~>aro.peaks</~~code~~> can be estimated from the aliphatic calibration. Typically the aromatic part of the simultaneous NOESY spectrum is less sensitive than the aromatic, therefore the values should be somewhat lower.		The <tt>sc</tt> and <tt>bb</tt> parameters for <tt>aro.peaks</tt> can be estimated from the aliphatic calibration. Typically the aromatic part of the simultaneous NOESY spectrum is less sensitive than the aromatic, therefore the values should be somewhat lower.

	<br>		<br>

	=== Verifying Initial NOE Calibration ===		=== Verifying Initial NOE Calibration ===

Jma at 23:45, 13 November 2009

2009-11-13T23:45:18Z

← Older revision		Revision as of 23:45, 13 November 2009
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	'''VERY IMPORTANT!!!'''. The default behavior of structure calculation (<~~code~~>anneal</~~code~~>, <~~code~~>calc_all</~~code~~>, <~~code~~>noeassign</~~code~~>) in CYANA 2.x is to use "sum of r<sup>-6</sup>" averaging for UPLs. Setting <~~code~~>expand=1</~~code~~> declares "sum of r<sup>-6</sup>" averaging, and <~~code~~>expand=0</~~code~~> declares "center" averaging. If you UPLs use "sum of r<sup>-6</sup>" averaging (if created with <~~code~~>peaks calibrate</~~code~~>), then		'''VERY IMPORTANT!!!'''. The default behavior of structure calculation (<tt>anneal</tt>, <tt>calc_all</tt>, <tt>noeassign</tt>) in CYANA 2.x is to use "sum of r<sup>-6</sup>" averaging for UPLs. Setting <tt>expand=1</tt> declares "sum of r<sup>-6</sup>" averaging, and <tt>expand=0</tt> declares "center" averaging. If you UPLs use "sum of r<sup>-6</sup>" averaging (if created with <tt>peaks calibrate</tt>), then

	*'''Do not''' use them with DYANA, CYANA 1.x and AutoStructure.		*'''Do not''' use them with DYANA, CYANA 1.x and AutoStructure.
	*'''Do not''' use them with legacy macros in CYANA 2.1, such as <~~code~~>habas</~~code~~>.		*'''Do not''' use them with legacy macros in CYANA 2.1, such as <tt>habas</tt>.
	*They can be used for manual structure calculation in CYANA 2.1, if <~~code~~>expand=1</~~code~~> is set before calling <~~code~~>anneal</~~code~~>.		*They can be used for manual structure calculation in CYANA 2.1, if <tt>expand=1</tt> is set before calling <tt>anneal</tt>.
	*They can be used for automated structure calculation in CYANA 2.1 with <~~code~~>noeassign</~~code~~>. The <~~code~~>noeassign</~~code~~> macro employs <~~code~~>peaks calibrate</~~code~~> (see below) and sets <~~code~~>expand=1</~~code~~>.		*They can be used for automated structure calculation in CYANA 2.1 with <tt>noeassign</tt>. The <tt>noeassign</tt> macro employs <tt>peaks calibrate</tt> (see below) and sets <tt>expand=1</tt>.

	<br>		<br>

	The aim of this new calibration method is likely to facilitate automated NOE assignment and structure calculation with <~~code~~>noeassign</~~code~~>. Unlike <~~code~~>caliba</~~code~~> and <~~code~~>calibrate</~~code~~>, <~~code~~>peaks calibrate</~~code~~> effectively generates UPLs even for unassigned peaks assuming NOEs between single protons. If such a peak gets assigned to a pseudoatom, the required correction is applied implicitly during the calculation.		The aim of this new calibration method is likely to facilitate automated NOE assignment and structure calculation with <tt>noeassign</tt>. Unlike <tt>caliba</tt> and <tt>calibrate</tt>, <tt>peaks calibrate</tt> effectively generates UPLs even for unassigned peaks assuming NOEs between single protons. If such a peak gets assigned to a pseudoatom, the required correction is applied implicitly during the calculation.

	<br>		<br>

	=== Initial NOE Calibration ===		=== Initial NOE Calibration ===

Jma at 23:42, 13 November 2009

2009-11-13T23:42:53Z

← Older revision		Revision as of 23:42, 13 November 2009
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	== '''References''' ==		== '''References''' ==

	1.   Wuthrich, K. (1986)  "NMR of Proteins and Nucleic Acids", page 127.		1.   Wuthrich, K. (1986)  "NMR of Proteins and Nucleic Acids", page 127.





			-- AlexEletski - 12 Jun 2007

			-- Edited by JimAramini - Nov 2009

Jma at 23:41, 13 November 2009

2009-11-13T23:41:20Z

Jma at 23:34, 13 November 2009

2009-11-13T23:34:41Z

← Older revision		Revision as of 23:34, 13 November 2009
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	NOE calibration converts NOESY cross-peak intensities into upper distance limits. A certain functional relationship is assumed between peak intensities and UPLs for a given group of peaks. The most common is NOE peak volume proportional to interproton distance to the minus six: <br>		NOE calibration converts NOESY cross-peak intensities into upper distance limits. A certain functional relationship is assumed between peak intensities and UPLs for a given group of peaks. The most common is NOE peak volume proportional to interproton distance to the minus six: <br>
	<pre> V = A/d^6</pre>		<pre> V = A/d^6</pre>
	where <~~code~~>V</~~code~~> is the peak volume (or intensity), <~~code~~>d</~~code~~> is the upper distance limit, and <~~code~~>A</~~code~~> is the calibration constant.		where <tt>V</tt> is the peak volume (or intensity), <tt>d</tt> is the upper distance limit, and <tt>A</tt> is the calibration constant.

	<br>		<br>
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	=== '''Command "calibrate"''' ===		=== '''Command "calibrate"''' ===

	A CYANA command <~~code~~>calibrate</~~code~~> is the basic calibration tool, unchanged since DYANA.		A CYANA command <tt>calibrate</tt> is the basic calibration tool, unchanged since DYANA.

	<br>		<br>
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	plot=file log minimal (default: none)		plot=file log minimal (default: none)
	</pre>		</pre>
	<~~code~~>calibrate</~~code~~> accepts a calibration function <~~code~~>f(d)</~~code~~> as the required argument.		<tt>calibrate</tt> accepts a calibration function <tt>f(d)</tt> as the required argument.

	This command uses "center" averaging. Explicit pseudoatom corrections are added to UPLs:		This command uses "center" averaging. Explicit pseudoatom corrections are added to UPLs:

	*Multiplicity correction is applied by dividing the peak volume by the numbers of 1H spins in pseudoatoms assigned to the peak. For instance, the volume of a cross peak between a Leu QQD pseudo atom and a Tyr QD pseudo atom is divided by a factor of 6 x 2 = 12 prior to applying the calibration function. The resulting UPL is the subject to the upper and lower cutoffs.		*Multiplicity correction is applied by dividing the peak volume by the numbers of 1H spins in pseudoatoms assigned to the peak. For instance, the volume of a cross peak between a Leu QQD pseudo atom and a Tyr QD pseudo atom is divided by a factor of 6 x 2 = 12 prior to applying the calibration function. The resulting UPL is the subject to the upper and lower cutoffs.
	*Distance correction is applied by adding a distance between the pseudoatom and its constituent spins. It is applied after the application of upper and lower cutoffs. For example, for a Tyr QD pseudoatom this correction is equal to half the distance between the HD1 and HD2 spins. Distance correction can be manually performed with the <~~code~~>distance correct</~~code~~> command.		*Distance correction is applied by adding a distance between the pseudoatom and its constituent spins. It is applied after the application of upper and lower cutoffs. For example, for a Tyr QD pseudoatom this correction is equal to half the distance between the HD1 and HD2 spins. Distance correction can be manually performed with the <tt>distance correct</tt> command.

	Type <~~code~~>help calibrate</~~code~~> at CYANA prompt for more information or see the DYANA documentation.		Type <tt>help calibrate</tt> at CYANA prompt for more information or see the DYANA documentation.

	<br>		<br>
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	=== '''Macro "caliba"''' ===		=== '''Macro "caliba"''' ===

	CYANA macro <~~code~~>caliba.cya</~~code~~> is functionally the same as <~~code~~>caliba.dya</~~code~~> of DYANA. It is a more sophisticated calibration tool aimed at getting more nuanced calibration than a uniform <code>1/d</code><sup><code>6</code></sup> dependence. CALIBA is recommended for manual structure calculation with CYANA 2.1. The <~~code~~>caliba</~~code~~> macro in fact uses <~~code~~>calibrate</~~code~~>, therefore, it also uses "center" averaging.		CYANA macro <tt>caliba.cya</tt> is functionally the same as <tt>caliba.dya</tt> of DYANA. It is a more sophisticated calibration tool aimed at getting more nuanced calibration than a uniform <code>1/d</code><sup><code>6</code></sup> dependence. CALIBA is recommended for manual structure calculation with CYANA 2.1. The <tt>caliba</tt> macro in fact uses <tt>calibrate</tt>, therefore, it also uses "center" averaging.

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			<br>

			== '''References''' ==
	== '''References''' ==

	1.   Wuthrich, K. (1986)  "NMR of Proteins and Nucleic Acids", page 127.		1.   Wuthrich, K. (1986)  "NMR of Proteins and Nucleic Acids", page 127.

Jma at 23:32, 13 November 2009

2009-11-13T23:32:41Z

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Jma at 23:30, 13 November 2009

2009-11-13T23:30:13Z

Show changes

← Older revision		Revision as of 23:49, 13 November 2009
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	The aim of this new calibration method is likely to facilitate automated NOE assignment and structure calculation with <tt>noeassign</tt>. Unlike <tt>caliba</tt> and <tt>calibrate</tt>, <tt>peaks calibrate</tt> effectively generates UPLs even for unassigned peaks assuming NOEs between single protons. If such a peak gets assigned to a pseudoatom, the required correction is applied implicitly during the calculation.		The aim of this new calibration method is likely to facilitate automated NOE assignment and structure calculation with <tt>noeassign</tt>. Unlike <tt>caliba</tt> and <tt>calibrate</tt>, <tt>peaks calibrate</tt> effectively generates UPLs even for unassigned peaks assuming NOEs between single protons. If such a peak gets assigned to a pseudoatom, the required correction is applied implicitly during the calculation.

	<br>		<br>

	=== Initial NOE Calibration ===		=== Initial NOE Calibration ===
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	After simulating and filtering one typically has three initial NOESY peaklists, for example, <tt>n.peaks</tt>, <tt>ali.peaks</tt>, and <tt>aro.peaks</tt>. The assigned peaks are intra-residue and short-range within secondary structure elements. Initial calibration is needed to verify these assignments for consistency with molecular geometry and, if possible, to derive stereospecific assignments with HABAS in CYANA. If your SequenceList and AtomList were generated with XEASY, you will need to convert them to the format of CYANA 2.1 (see the <tt>~/demo/details/MigrateFromDyanaCyana1.cya</tt> example script). SequenceList and AtomList from CARA are already compatible.		After simulating and filtering one typically has three initial NOESY peaklists, for example, <tt>n.peaks</tt>, <tt>ali.peaks</tt>, and <tt>aro.peaks</tt>. The assigned peaks are intra-residue and short-range within secondary structure elements. Initial calibration is needed to verify these assignments for consistency with molecular geometry and, if possible, to derive stereospecific assignments with HABAS in CYANA. If your SequenceList and AtomList were generated with XEASY, you will need to convert them to the format of CYANA 2.1 (see the <tt>~/demo/details/MigrateFromDyanaCyana1.cya</tt> example script). SequenceList and AtomList from CARA are already compatible.

	Amide, aliphatic and aromatic protons tend to have different relaxation properties in a simultaneous 3D ~~15N~~-, ~~13C~~-resolved NOESY.  NOESY spectra acquired separately may have varying acquisition times. Therefore, it is recommended to run <tt>caliba</tt> separately for each peaklist.		Amide, aliphatic and aromatic protons tend to have different relaxation properties in a simultaneous 3D <sup>15</sup>N-, <sup>13</sup>C-resolved NOESY.  NOESY spectra acquired separately may have varying acquisition times. Therefore, it is recommended to run <tt>caliba</tt> separately for each peaklist.

	Here is a sample [[Media:Run_caliba.cya\|run_caliba.cya]] script for running <tt>caliba</tt> on all three peaklists:		Here is a sample [[Media:Run_caliba.cya\|run_caliba.cya]] script for running <tt>caliba</tt> on all three peaklists:
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	The <tt>sc</tt> and <tt>bb</tt> parameters for <tt>aro.peaks</tt> can be estimated from the aliphatic calibration. Typically the aromatic part of the simultaneous NOESY spectrum is less sensitive than the aromatic, therefore the values should be somewhat lower.		The <tt>sc</tt> and <tt>bb</tt> parameters for <tt>aro.peaks</tt> can be estimated from the aliphatic calibration. Typically the aromatic part of the simultaneous NOESY spectrum is less sensitive than the aromatic, therefore the values should be somewhat lower.

	<br>		<br>

	=== Verifying Initial NOE Calibration ===		=== Verifying Initial NOE Calibration ===
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	1.   Wuthrich, K. (1986)  "NMR of Proteins and Nucleic Acids", page 127.		1.   Wuthrich, K. (1986)  "NMR of Proteins and Nucleic Acids", page 127.

			<br>

			<br>

			-- AlexEletski - 12 Jun 2007

	-- AlexEletski - 12 Jun 2007

	-- Edited by JimAramini - Nov 2009		-- Edited by JimAramini - Nov 2009

← Older revision		Revision as of 23:41, 13 November 2009
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	By default, constant <~~code~~>A</~~code~~> is calculated from <~~code~~>avedis</~~code~~> - the assumed average distance between backbone atoms. It is also possible to specify the backbone constant <~~code~~>A</~~code~~> explicitly. Constant <~~code~~>B</~~code~~> is then calculated from <~~code~~>A</~~code~~>, and <~~code~~>C</~~code~~> from <~~code~~>B</~~code~~>		By default, constant <tt>A</tt> is calculated from <tt>avedis</tt> - the assumed average distance between backbone atoms. It is also possible to specify the backbone constant <tt>A</tt> explicitly. Constant <tt>B</tt> is then calculated from <tt>A</tt>, and <tt>C</tt> from <tt>B</tt>

	Parameters <~~code~~>dmin</~~code~~> and <~~code~~>dmax</~~code~~> are the lower and upper cutoff limits for UPLs, respectively.		Parameters <tt>dmin</tt> and <tt>dmax</tt> are the lower and upper cutoff limits for UPLs, respectively.

	Parameter <~~code~~>vmin</~~code~~> is useful to filter out peaks with intensities below a certain threshold. Without it even incorrectly picked peaks with intensities below S/N level will produce UPLs set at the upper cutoff.		Parameter <tt>vmin</tt> is useful to filter out peaks with intensities below a certain threshold. Without it even incorrectly picked peaks with intensities below S/N level will produce UPLs set at the upper cutoff.

	<~~code~~>plot</~~code~~> is an optional parameter, used to create logarithmic plots of volumes versus corresponding minimal distances in the selected structures together with the calibration functions. It is useful for fine-tuning the calibration during structure refinement. Of course, a structure must be then loaded into CYANA before running <~~code~~>caliba</~~code~~>.		<tt>plot</tt> is an optional parameter, used to create logarithmic plots of volumes versus corresponding minimal distances in the selected structures together with the calibration functions. It is useful for fine-tuning the calibration during structure refinement. Of course, a structure must be then loaded into CYANA before running <tt>caliba</tt>.

	<br> '''VERY IMPORTANT!!!'''. The default behavior of structure calculation (<~~code~~>anneal</~~code~~>, <~~code~~>calc_all</~~code~~>, <~~code~~>noeassign</~~code~~>) in CYANA 2.x is to use "sum of r<sup>-6</sup>" averaging for UPLs. Setting <~~code~~>expand=1</~~code~~> declares "sum of r<sup>-6</sup>" averaging, and <~~code~~>expand=0</~~code~~> declares "center" averaging. If your UPLs reflect "center" averaging (that is, they were created with <~~code~~>caliba</~~code~~> or <~~code~~>calibrate</~~code~~>), then		<br> '''VERY IMPORTANT!!!'''. The default behavior of structure calculation (<tt>anneal</tt>, <tt>calc_all</tt>, <tt>noeassign</tt>) in CYANA 2.x is to use "sum of r<sup>-6</sup>" averaging for UPLs. Setting <tt>expand=1</tt> declares "sum of r<sup>-6</sup>" averaging, and <tt>expand=0</tt> declares "center" averaging. If your UPLs reflect "center" averaging (that is, they were created with <tt>caliba</tt> or <tt>calibrate</tt>), then

	*They can be used with DYANA, CYANA 1.x and AutoStructure.		*They can be used with DYANA, CYANA 1.x and AutoStructure.
	*They can be used with legacy macros in CYANA 2.1, such as <~~code~~>habas</~~code~~>.		*They can be used with legacy macros in CYANA 2.1, such as <tt>habas</tt>.
	*They can be used for manual structure calculation in CYANA 2.1, if <~~code~~>expand=0</~~code~~> is set before calling <code>anneal</code>.		*They can be used for manual structure calculation in CYANA 2.1, if <tt>expand=0</tt> is set before calling <code>anneal</code>.
	*'''Do not''' use them for automated structure calculation in CYANA 2.1 with <~~code~~>noeassign</~~code~~>. The <~~code~~>noeassign</~~code~~> macro employs <~~code~~>peaks calibrate</~~code~~> (see below) and sets <~~code~~>~~exapand~~=1</~~code~~>. In general, '''do not''' mix them with UPLs calibrated with <~~code~~>peaks calibrate</~~code~~>.		*'''Do not''' use them for automated structure calculation in CYANA 2.1 with <tt>noeassign</tt>. The <tt>noeassign</tt> macro employs <tt>peaks calibrate</tt> (see below) and sets <tt>expand=1</tt>. In general, '''do not''' mix them with UPLs calibrated with <tt>peaks calibrate</tt>.

	Type <~~code~~>help caliba</~~code~~> at CYANA prompt or see the DYANA manual for more information. You can also look at the script itself in the <~~code~~>macro</~~code~~> subdirectory of a CYANA installation.		Type <tt>help caliba</tt> at CYANA prompt or see the DYANA manual for more information. You can also look at the script itself in the <tt>macro</tt> subdirectory of a CYANA installation.

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	=== '''Command "peaks calibrate"''' ===		=== '''Command "peaks calibrate"''' ===

	Command <~~code~~>peaks calibrate</~~code~~> is a new feature of CYANA 2.x, which produced a "sum of r<sup>-6</sup>"-averaged calibration. The documentation for it is scarce. For example, the manual structure calculation script <~~code~~>~/demo/manual/CALC.cya</~~code~~> contains these lines:		Command <tt>peaks calibrate</tt> is a new feature of CYANA 2.x, which produced a "sum of r<sup>-6</sup>"-averaged calibration. The documentation for it is scarce. For example, the manual structure calculation script <tt>~/demo/manual/CALC.cya</tt> contains these lines:

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	write upl $name-in.upl		write upl $name-in.upl
	</pre>		</pre>
	Line <~~code~~>calibration prot=$prot peaks=$peaks constant=$calibration dref=$dref</~~code~~> calls the macro <~~code~~>calibration.cya</~~code~~>, which iteratively sets calibration constants for each peaklist. If the <~~code~~>calibration</~~code~~> list variable is defined, its values are taken as calibration constants. If it is left blank, calibration constants are calibrated based on assumed average distance <~~code~~>dref</~~code~~> between '''all''' atoms of the molecule. Note that <~~code~~>dref</~~code~~> here is inherently different from <~~code~~>avedis</~~code~~> of <~~code~~>caliba</~~code~~> - the latter refers only to distances between <~~code~~>backbone</~~code~~> protons.		Line <tt>calibration prot=$prot peaks=$peaks constant=$calibration dref=$dref</tt> calls the macro <tt>calibration.cya</tt>, which iteratively sets calibration constants for each peaklist. If the <tt>calibration</tt> list variable is defined, its values are taken as calibration constants. If it is left blank, calibration constants are calibrated based on assumed average distance <tt>dref</tt> between '''all''' atoms of the molecule. Note that <tt>dref</tt> here is inherently different from <tt>avedis</tt> of <tt>caliba</tt> - the latter refers only to distances between <tt>backbone</tt> protons.

	Line <~~code~~>peaks calibrate "**" simple</~~code~~> generates UPLs assuming simple <~~code~~>C/d^6</~~code~~> functions with calibration constants <~~code~~>C</~~code~~> from the previous step. These calibration constants are thus closely related the "backbone" class constants <~~code~~>A</~~code~~> of <~~code~~>caliba</~~code~~>.		Line <tt>peaks calibrate "**" simple</tt> generates UPLs assuming simple <tt>C/d^6</tt> functions with calibration constants <tt>C</tt> from the previous step. These calibration constants are thus closely related the "backbone" class constants <tt>A</tt> of <tt>caliba</tt>.

	To modify upper and lower cutoffs for NOE calibration with <~~code~~>peaks calibrate</~~code~~> add a line <~~code~~>set upl_values:=2.4,6.0</~~code~~>. The defaults are 2.4 and 5.5.		To modify upper and lower cutoffs for NOE calibration with <tt>peaks calibrate</tt> add a line <tt>set upl_values:=2.4,6.0</tt>. The defaults are 2.4 and 5.5.

	The main difference from <~~code~~>calibrate</~~code~~> and <~~code~~>caliba</~~code~~> is that pseudoatom correction are '''not applied''' to resulting UPLs.		The main difference from <tt>calibrate</tt> and <tt>caliba</tt> is that pseudoatom correction are '''not applied''' to resulting UPLs.

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