Alex at 19:35, 18 October 2011

2011-10-18T19:35:21Z

← Older revision		Revision as of 19:35, 18 October 2011
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			One can start either by creating an empty peaklist, or by exporting inferred peak and spinliks from PolyScope. After that it is possible to add peaks interactively or with a script. The fastest method seems to be picking peaks automaticaly with the 'PickAll3DNOESY' script from an empty peaklist.

			== '''Simulate short and sequential peaks''' ==

	# Run 'ExportToCSI' script to generate an input file for CSI		# Run 'ExportToCSI' script to generate an input file for CSI
	# Run CSI program		# Run the CSI program
	# Run the 'CreateShortSequentialSpinLinks' script to generate spin-links based on CSI prediction		# Run the 'CreateShortSequentialSpinLinks' script to generate spin-links based on CSI prediction
	# Remove all unnecessary spins, such as draft assignments (e.g. '?HA'), projected spins (e.g. 'HA-1') and GFT pseudospins (e.g. 'CApCB'). Bulk remove is possible with scripts such as RemoveSins, RemoveProjectedSpins and RemoveGFTSpins.		# Remove all unnecessary spins, such as draft assignments (e.g. '?HA'), projected spins (e.g. 'HA-1') and GFT pseudospins (e.g. 'CApCB'). Bulk remove is possible with scripts such as RemoveSins, RemoveProjectedSpins and RemoveGFTSpins.
	# Open an HSQC spectrum in PolyScope window with the corresponding NOESY spectrum loaded in the strip. In the 'Strip' menu make sure that the 'Show Spin Links' box is ~~check~~, and the 'Show Inferred Peaks' is unchecked. Select 'File' -> 'Export...' -> 'Strip Peaks to MonoScope...' to create an initial peaklist with existing assignments.		# Open an HSQC spectrum in PolyScope window with the corresponding NOESY spectrum loaded in the strip. In the 'Strip' menu make sure that the 'Show Spin Links' box is checked, and the 'Show Inferred Peaks' is unchecked. Select 'File' -> 'Export...' -> 'Strip Peaks to MonoScope...' to create an initial peaklist with existing assignments.
	~~# Many predicted~~ peaks ~~may not be actually observed~~. Therefore, integrate the peak list first and then use the PeakListReport script to delete all peaks weaker than a certain threshold.

			* Note that certain spinlinks (such as HE <-> N in Lys, for example) will yield undetectable peaks. Therefore, integrate the peak list first and then use the 'PeakListReport' script to delete all peaks weaker than a certain threshold.
			* Some peaks may have significant overlap, or have contributions from yet unassigned long-range peaks. Interactive refinement is necessary.

	Automated peak picking		== '''Automated peak picking''' ==

	# ~~Define~~ the peak linewidths in ~~the peak model for the peak list of interest~~.		# For each peaklist define the typical peak linewidths using '''Intergrate -> Tune Peak Model...''' in MonoScope.
	# Set 'DeafultPeaklist' and 'PeakListToSpectrumMapping' attributes of the corresponding spectrum according to the peaklist.		# Set 'DeafultPeaklist' and 'PeakListToSpectrumMapping' attributes of the corresponding spectrum according to the peaklist.
	# Run the PickAll3DNOESY script to automatically pick peaks.		# Run the 'PickAll3DNOESY' script to automatically pick peaks.
	# Run the 'PeakListReport' script to delete diagonal peaks.		# Run the 'PeakListReport' script to delete diagonal peaks.
	# Refine the resulting peaklist by interactivelly scanning all strips.		# Refine the resulting peaklist by interactivelly scanning all strips.

Alex: Created page with '# Run 'ExportToCSI' script to generate an input file for CSI # Run CSI program # Run the 'CreateShortSequentialSpinLinks' script to generate spin-links based on CSI prediction # …'

2011-04-23T15:57:20Z

Created page with '# Run 'ExportToCSI' script to generate an input file for CSI # Run CSI program # Run the 'CreateShortSequentialSpinLinks' script to generate spin-links based on CSI prediction # …'

New page

# Run 'ExportToCSI' script to generate an input file for CSI
# Run CSI program
# Run the 'CreateShortSequentialSpinLinks' script to generate spin-links based on CSI prediction
# Remove all unnecessary spins, such as draft assignments (e.g. '?HA'), projected spins (e.g. 'HA-1') and GFT pseudospins (e.g. 'CApCB'). Bulk remove is possible with scripts such as RemoveSins, RemoveProjectedSpins and RemoveGFTSpins.
# Open an HSQC spectrum in PolyScope window with the corresponding NOESY spectrum loaded in the strip. In the 'Strip' menu make sure that the 'Show Spin Links' box is check, and the 'Show Inferred Peaks' is unchecked. Select 'File' -> 'Export...' -> 'Strip Peaks to MonoScope...' to create an initial peaklist with existing assignments.
# Many predicted peaks may not be actually observed. Therefore, integrate the peak list first and then use the PeakListReport script to delete all peaks weaker than a certain threshold.

Automated peak picking

# Define the peak linewidths in the peak model for the peak list of interest.
# Set 'DeafultPeaklist' and 'PeakListToSpectrumMapping' attributes of the corresponding spectrum according to the peaklist.
# Run the PickAll3DNOESY script to automatically pick peaks.
# Run the 'PeakListReport' script to delete diagonal peaks.
# Refine the resulting peaklist by interactivelly scanning all strips.

Creating NOESY peaklists with CARA - Revision history

Alex at 19:35, 18 October 2011

Alex: Created page with '# Run 'ExportToCSI' script to generate an input file for CSI # Run CSI program # Run the 'CreateShortSequentialSpinLinks' script to generate spin-links based on CSI prediction # …'