ENORA and multi-state structure calculations - Revision history

Dean: /* Exercise: Setting up a two-state calculation */

2021-03-18T14:11:22Z

Exercise: Setting up a two-state calculation

← Older revision		Revision as of 16:11, 18 March 2021
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	When you are done preparing the macros as outlined perform the calculation by running the 'CALC_multistate.cya' macro:		When you are done preparing the macros as outlined perform the calculation by running the 'CALC_multistate.cya' macro:

	cyana ~~-n 33~~ CALC_multistate~~.cya~~.cya		cyana CALC_multistate.cya

	Carefully analyze the WARNING and ERROR messages if any.		Carefully analyze the WARNING and ERROR messages if any.

Dean: /* Exercise: Setting up a two-state calculation */

2021-03-18T14:10:48Z

Exercise: Setting up a two-state calculation

← Older revision		Revision as of 16:10, 18 March 2021
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	With a text editor, change the number of states (nbundle=@i=) from one to two in the 'PREP.cya' macro:		With a text editor, change the number of states (nbundle=@i=) from one to two in the 'PREP.cya' macro:

	syntax nbundle=@i=1 togetherweight=@r=0.1 multitensor		syntax nbundle=@i=2 togetherweight=@r=0.1 multitensor

	When you are done preparing the macros as outlined perform the calculation by running the 'CALC_multistate.cya' macro:		When you are done preparing the macros as outlined perform the calculation by running the 'CALC_multistate.cya' macro:

Dean: /* Calculating a single state structure */

2021-03-18T14:09:27Z

Calculating a single state structure

← Older revision		Revision as of 16:09, 18 March 2021
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	weight_aco = 0.0		weight_aco = 0.0

	rmsdrange:=8-33~~,108-133~~		rmsdrange:=8-33
	overview sstate structures=20 pdb		overview sstate structures=20 pdb
	end if		end if

Dean at 13:12, 18 March 2021

2021-03-18T13:12:28Z

Dean: /* The eNORA CALC macro */

2020-08-06T10:06:57Z

The eNORA CALC macro

← Older revision		Revision as of 12:06, 6 August 2020
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	# fit experimental buildups		# fit experimental buildups
	[[CYANA Command: enoe sig \|enoe ~~sigma~~]] opt=1		[[CYANA Command: enoe sig \|enoe sig]] opt=1

	# ---------------------------------- spin-diffusion ----------------------------------		# ---------------------------------- spin-diffusion ----------------------------------
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	# apply spin-diffusion correction to experimental buildups (if calculated) and calculate sigma		# apply spin-diffusion correction to experimental buildups (if calculated) and calculate sigma
	[[CYANA Command: enoe sig \|enoe ~~sigma~~]] opt=2		[[CYANA Command: enoe sig \|enoe sig]] opt=2

	# calculate reff		# calculate reff

Dean: /* The eNORA CALC macro */

2020-08-06T10:06:03Z

The eNORA CALC macro

← Older revision		Revision as of 12:06, 6 August 2020
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	# fit experimental buildups		# fit experimental buildups
	[[CYANA Command: enoe cross \|enoe cross]]		[[CYANA Command: enoe cross \|enoe cross]]
	[[CYANA Command: enoe sig \|enoe ~~sigma~~]] opt=1		[[CYANA Command: enoe sig \|enoe sig]] opt=1

	# ---------------------------------- spin-diffusion ----------------------------------		# ---------------------------------- spin-diffusion ----------------------------------
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	# apply spin-diffusion correction to experimental buildups (if calculated) and calculate sigma		# apply spin-diffusion correction to experimental buildups (if calculated) and calculate sigma
	[[CYANA Command: enoe sig \|enoe ~~sigma~~]] opt=2		[[CYANA Command: enoe sig \|enoe sig]] opt=2

	# calculate reff		# calculate reff

Dean: /* Generating XEASY peak list with expected FRM or two-spin intensities */

2020-02-19T15:50:39Z

Generating XEASY peak list with expected FRM or two-spin intensities

← Older revision		Revision as of 17:50, 19 February 2020
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	enoe spindiff b0field=b0field time=$mixingtimes(n) mode=3 labilatom='NONE'		enoe spindiff b0field=b0field time=$mixingtimes(n) mode=3 labilatom='NONE'
	enoe twospin b0field=b0field time=$mixingtimes(n) mode=3 labilatom='NONE'		enoe twospin b0field=b0field time=$mixingtimes(n) mode=3 labilatom='NONE'
			# FM
	read peaks N15NOESY_exp.peaks		read peaks N15NOESY_exp.peaks
	~~# FM~~
	[[CYANA Command: enoe values\|enoe values]] mode=1		[[CYANA Command: enoe values\|enoe values]] mode=1
	write peaks N15NOESY_FM_$n.peaks names		write peaks N15NOESY_FM_$n.peaks names
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	write peaks C13NOESY_FM_$n.peaks names		write peaks C13NOESY_FM_$n.peaks names
	# 2 spin		# 2 spin
			read peaks N15NOESY_exp.peaks
	[[CYANA Command: enoe values\|enoe values]] mode=2		[[CYANA Command: enoe values\|enoe values]] mode=2
	write peaks N15NOESY_2spin_$n.peaks names		write peaks N15NOESY_2spin_$n.peaks names

Dean: /* Generating XEASY peak list with expected FRM or two-spin intensities */

2020-02-19T15:48:39Z

Generating XEASY peak list with expected FRM or two-spin intensities

← Older revision		Revision as of 17:48, 19 February 2020
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	do n 1 length('mixingtimes')		do n 1 length('mixingtimes')

	enoe spindiff b0field=b0field time=$mixingtimes(n) mode=3 labilatom='NONE'		enoe spindiff b0field=b0field time=$mixingtimes(n) mode=3 labilatom='NONE'
	enoe twospin b0field=b0field time=$mixingtimes(n) mode=3 labilatom='NONE'		enoe twospin b0field=b0field time=$mixingtimes(n) mode=3 labilatom='NONE'

Dean: /* Generating XEASY peak list with expected FRM or two-spin intensities */

2020-02-19T13:28:28Z

Generating XEASY peak list with expected FRM or two-spin intensities

← Older revision		Revision as of 15:28, 19 February 2020
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	read peaks N15NOESY_exp.peaks		read peaks N15NOESY_exp.peaks
	# FM		# FM
	[[CYANA Command: ~~atoms~~ values\|~~atoms~~ values]] mode=1		[[CYANA Command: enoe values\|enoe values]] mode=1
	write peaks N15NOESY_FM_$n.peaks names		write peaks N15NOESY_FM_$n.peaks names
	read peaks C13NOESY_exp.peaks		read peaks C13NOESY_exp.peaks

Dean: /* Generating XEASY peak list with expected FRM or two-spin intensities */

2020-02-19T13:27:59Z

Generating XEASY peak list with expected FRM or two-spin intensities

← Older revision		Revision as of 15:27, 19 February 2020
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	write peaks N15NOESY_FM_$n.peaks names		write peaks N15NOESY_FM_$n.peaks names
	read peaks C13NOESY_exp.peaks		read peaks C13NOESY_exp.peaks
	[[CYANA Command: ~~atoms~~ values\|~~atoms~~ values]] mode=1		[[CYANA Command: enoe values\|enoe values]] mode=1
	write peaks C13NOESY_FM_$n.peaks names		write peaks C13NOESY_FM_$n.peaks names
	# 2 spin		# 2 spin
	[[CYANA Command: ~~atoms~~ values\|~~atoms~~ values]] mode=2		[[CYANA Command: enoe values\|enoe values]] mode=2
	write peaks N15NOESY_2spin_$n.peaks names		write peaks N15NOESY_2spin_$n.peaks names
	read peaks C13NOESY_exp.peaks		read peaks C13NOESY_exp.peaks
	[[CYANA Command: ~~atoms~~ values\|~~atoms~~ values]] mode=2		[[CYANA Command: enoe values\|enoe values]] mode=2
	write peaks C13NOESY_2spin_$n.peaks names		write peaks C13NOESY_2spin_$n.peaks names
	end do		end do

← Older revision		Revision as of 15:12, 18 March 2021
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	#INAME 2 HN		#INAME 2 HN
	#INAME 3 N		#INAME 3 N
	#SPECTRUM N15NOESY H HN N ~~??? change to 13C, processed as 13C!!!!~~		#SPECTRUM N15NOESY H HN N
	17086 4.098 4.099 57.441 1 U 6.990943E+08 0.000000E+00 e 0 HA.5 HA.5 CA.5		17086 4.098 4.099 57.441 1 U 6.990943E+08 0.000000E+00 e 0 HA.5 HA.5 CA.5
	89532 4.355 1.829 33.507 1 U 1.720779E+06 0.000000E+00 e 0 HA.6 HB2.6 CB.6		89532 4.355 1.829 33.507 1 U 1.720779E+06 0.000000E+00 e 0 HA.6 HB2.6 CB.6
	89544 4.353 1.757 33.513 1 U 2.939628E+06 0.000000E+00 e 0 HA.6 HB3.6 CB.6		89544 4.353 1.757 33.513 1 U 2.939628E+06 0.000000E+00 e 0 HA.6 HB3.6 CB.6

	The first line specifies the number of dimensions (3 in this case). The '#SPECTRUM' (no space between characters) lines gives the experiment type (N15NOESY, which refers to the corresponding experiment definition in the CYANA library), followed by an identifier for each dimension of the peak list (H HN N) that specifies which chemical shift is stored in the corresponding dimension of the peak list. The experiment type and identifiers must correspond to an experiment definition in the general CYANA library (see below) in most uses of the definition, here however we cheat slightly because for eNOE calculations we record our NOESY spectra with ~~simultanous~~ evolution of 13C and 15N dimensions, since we require 15N and 13C bound spins within the same spectrum for purposes of normalization (see...).		The first line specifies the number of dimensions (3 in this case). The '#SPECTRUM' (no space between characters) lines gives the experiment type (N15NOESY, which refers to the corresponding experiment definition in the CYANA library), followed by an identifier for each dimension of the peak list (H HN N) that specifies which chemical shift is stored in the corresponding dimension of the peak list. The experiment type and identifiers must correspond to an experiment definition in the general CYANA library (see below) in most uses of the definition, here however we cheat slightly because for eNOE calculations we record our NOESY spectra with simultaneous evolution of 13C and 15N dimensions, since we require 15N and 13C bound spins within the same spectrum for purposes of normalization (see...).

	After the '#SPECTRUM' line follows one line for every peak. For example, the first peak in the 'HNCA.peaks' list has		After the '#SPECTRUM' line follows one line for every peak. For example, the first peak in the 'HNCA.peaks' list has
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	* Heavy atom chemical shift 57.441 ppm (in this case 13C labeled)		* Heavy atom chemical shift 57.441 ppm (in this case 13C labeled)

	The other data are relevant entry for the eNOE ~~mudules~~ is the peak volume or intensity (6.990943E+08).		The other data are relevant entry for the eNOE modules is the peak volume or intensity (6.990943E+08).

	==== SPECTRUM definitions in the CYANA library ====		==== SPECTRUM definitions in the CYANA library ====
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	The first line corresponds to the '#SPECTRUM' line in the peak list. It specifies the experiment name and identifies the atoms that are detected in each dimension of the spectrum. The number of identifiers defines the dimensionality of the experiment (3 in case of N15NOESY).		The first line corresponds to the '#SPECTRUM' line in the peak list. It specifies the experiment name and identifies the atoms that are detected in each dimension of the spectrum. The number of identifiers defines the dimensionality of the experiment (3 in case of N15NOESY).

	Each ~~line below~~ defines a (formal) magnetization transfer pathway that gives rise to an expected peak. in the case of N15NOESY there are five lines, corresponding to the through space magnetization transfer by dipol-dipol mechanism. The peak definition starts with the probability to observe the peak (0.900), followed by a series of atom types, e.g. H_AMI for amide proton etc. The atoms whose chemical shifts appear in the spectrum are identified by their labels followed by ':', e.g. for N15NOESY 'H:', 'HN:', and 'N:'. If you were to use the CYANA functions to simulate peaks, expected peaks are generated for each molecular fragment in which these atom types occur.		Each of the following lines defines a (formal) magnetization transfer pathway that gives rise to an expected peak. in the case of N15NOESY there are five lines, corresponding to the through space magnetization transfer by dipol-dipol mechanism. The peak definition starts with the probability to observe the peak (0.900), followed by a series of atom types, e.g. H_AMI for amide proton etc. The atoms whose chemical shifts appear in the spectrum are identified by their labels followed by ':', e.g. for N15NOESY 'H:', 'HN:', and 'N:'. If you were to use the CYANA functions to simulate peaks, expected peaks are generated for each molecular fragment in which these atom types occur.

	You may have realized that our peak list contains peaks that are 13C bound, therefore the spectrum definition is wrong, since we are only reading the peak lists and not generating any, this is not a problem.		You may have realized that our peak list contains peaks that are 13C bound, therefore the spectrum definition is wrong, since we are only reading the peak lists and not generating any, this is not a problem.