Detken, A; Hardy, EH; Ernst, M; Kainosho, M; Kawakami, T; Aimoto, S & Meier BH. J. Biomol. NMR 20, 203-221 (2001)
2D Triple Resonance
Sun, BO; Rienstra, CM; Costa, PR; Williamson, JR & Griffin RG. J. Am. Chem. Soc. 119, 8540-8546 (1997)
3D Triple Resonance
Sun, BO; Rienstra, CM; Costa, PR; Williamson, JR & Griffin RG. J. Am. Chem. Soc. 119, 8540-8546 (1997)
3D Triple Resonance
To use 2D NCA for navigation in PolyScope, first open NCACX with PolyScopeRotated and select x-axis=N, y-axis=CA, z-axis (depth)=CX. Then select the 2D NCA in the Plane-Select Spectrum menu.
Schaefer, J; McKay, RA & Stejskal, EO. J. Magn. Reson, 34, 443-447 (1979)
Baldus, M; Geurts, DG; Hediger, S & Meier BH. J. Magn Reson. A, 118, 140-144 (1996)
2D Triple Resonance
Schaefer, J; McKay, RA & Stejskal, EO. J. Magn. Reson, 34, 443-447 (1979)
Baldus, M; Petkova, AT; Herzfeld, J & Griffin, RG. Mol. Phys. 95, 1197-1207 (1998)
2D Triple Resonance
CA is along y-axis to facilitate synchronization with scopes using strips.
Schaefer, J; McKay, RA & Stejskal, EO. J. Magn. Reson, 34, 443-447 (1979)
Baldus, M; Petkova, AT; Herzfeld, J & Griffin, RG. Mol. Phys. 95, 1197-1207 (1998)
2D Triple Resonance
Boembergen, N; Purcell, EM & Pund, RV. Physical Review 73, 679-712 (1948)
2D Homonuclear
Can be used for all through-space homonuclear transfer sequences (e.g. PDSD/DARR, RFDR, DREAM etc.)
Baldus, M & Meier BH. J. Magn. Reson. A, 121, 65-69 (1996)
2D Homonuclear
Can be used for all through-bond transfere techniques, as well as through-space transfer techniques (e.g. PDSD) with short mixing times.
2D Double Resonance
Straus, SK; Bremi, T & Ernst R. J. Biomol. NMR 12, 39-50 (1998)
2D Triple Resonance
Straus, SK; Bremi, T & Ernst R. J. Biomol. NMR 12, 39-50 (1998)
2D Triple Resonance
Boembergen, N; Purcell, EM & Pund, RV. Physical Review 73, 679-712 (1948)
2D Homonuclear
1D Homonuclear
Y. Li, D.A. Berthold, H.L. Frericks, R.B. Gennis, C.M. Rienstra, Chem. Biochem. 8 434-442 (2007).
3D Triple Resonance
Boembergen, N; Purcell, EM & Pund, RV. Physical Review 73, 679-712 (1948)
2D Homonuclear
Can be used for all through-space homonuclear transfer sequences (e.g. PDSD/DARR, RFDR, DREAM etc.)
01-23-2013
4.000000
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
01-23-2013
4.0
2013-2-5
Based on:
ProteinSolidState1.0v1.cara
This template is intended for resonance assignment of 13C/15N-labeled proteins using solid state NMR. CLICK IN WINDOW TO SEE MORE INFO.
Object Tables:
ResidueType, Spectrum and SpectrumType have Attributes which can be viewed from the corresponding Cara explorer window using "Open Object Table".
----------------------------------------------------------
Residue Types:
- ResidueTypes include all the standard amino acid residues in IUPAC nomenclature for compatibility with BMRB.
- Chemical shifts reflect the diamagnetic protein statistics of the BMRB of Jan-23-2013. See ObjectTable for the date and SDmult used.
Spectrum Types:
- Typically used in assignment of proteins for solid state are included. Right-click on the SpectrumType and select Edit Attributes or Open Object Table to get more information.
- The SpectrumTypes are defined so that the C13 dimensions are oriented along the long axis of the strips. This leads to some unconventional orientations. E.g. the NCA has the N along the horizontal axis. The advantage is that the vertical axis which contains CA can be synchronized with the strips vertical axes in 3D spectra which are displayed in StripScope, SystemScope, and PolyScope.
- To obtain a correct orientation for NCACX in PolyScope, open it with PolyScopeRotated and select X-axis=N,Y-axis(height)=CA,Z-axis(depth)=CX. Then select the NCA in the Planes-Select Spectrum menu.
- FEEDBACK on this approach or alternatives is welcome!
Spin System Types:
- available types are now all ResidueTypes. Select the SpinSystemType to expand the available set of labels when you are not yet 100% sure
about which ResidueType the SpinSystem is.
Terminal:
- included both new and updated scripts. For a description of their function, click on the script and right-click "Edit Attributes". For more details "Open" the script and read the header.
-----------------------------------------------------------
conversion scripts
- BMRB file to Project:
1) read in a BMRB str file as a project by using the standard menu item "Project-Import Project from BMRB". Note that NmrStar 3.1 is not supported.
2) Afterwards run the script "ReplaceDegenerateSpinsByGroup.lua" to remove the degenerate spins from the BMRB file (see "Edit Attributes" or the header to script for details)
- importing Xeasy files to ProteinSolidState1.0v1.cara :
1) convert sequence file to cara template-compatible format (only three letter code allowed) using LUA script XeasySeqTo3Letter.lua
2) convert protonlist file to cara template-compatible format (e.g. HN -> H) using LUA script XeasyToBmrbLabelsInProtonList.lua
3) Load these into a new project using "Project-Import Project From Sequence" and "ProjectName-Import AtomList".
4) To import Alias shifts to the new project, use the LUA script "PeakListToAliases.lua"
- Cara Project to BMRB deposit (chemical shifts only)
1) Run AssignmentReport.lua to check for inconsistencies and unusual shifts. Correct problems in the assignments.
2) Run the LUA script WriteAssignments.lua and select output format BMRB.
- Structure calculation
1) Run the LUA script AssignmentReport.lua and fix any problems in the assignments (see above)
2) Run the LUA script WriteAssignments.lua and select output format corresponding to your structure calculation program (e.g. DYANA/CYANA1)
2013-1-30
2013-2-5
true
Fred Damberger
ProteinSolidState1.0v2.cara
Fred Damberger, Ansgar Siemer, Sebastian Hiller
Fred Damberger, Ansgar Siemer