Automated resonance assignment with FLYA (EMBO 2013): Difference between revisions
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We want to determine the resonance assignments and the structure of a protein. | We want to determine the resonance assignments and the structure of a protein. | ||
== Experimental input data == | |||
The protein sequence is stored in the file 'demo.seq'. | The protein sequence is stored in the file 'demo.seq'. | ||
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7 6.475 54.017 98.159 1 U 2.547E+01 0.000E+00 e 0 0 0 0 | 7 6.475 54.017 98.159 1 U 2.547E+01 0.000E+00 e 0 0 0 0 | ||
The first line specifies the number of dimensions (3 in this case). The '#SPECTRUM' lines gives the experiment type (HNCA), followed by an identifier for each dimension of the peak list (HN C N) that specifies which chemical shift is stored in the corresponding dimension of the peak list. Below follows one for every peak. For example, the first peak in the HNCA.peaks list has | The first line specifies the number of dimensions (3 in this case). The '#SPECTRUM' lines gives the experiment type (HNCA, which refers to the corresponding experiment definition in the CYANA library), followed by an identifier for each dimension of the peak list (HN C N) that specifies which chemical shift is stored in the corresponding dimension of the peak list. Below follows one for every peak. For example, the first peak in the HNCA.peaks list has | ||
* Peak number 5 | * Peak number 5 | ||
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The other data are irrelevant for automated chemical shift assignment with FLYA. In particular, the peak volume or intensity (2.769E+02) is ''not'' used by the algorithm. | The other data are irrelevant for automated chemical shift assignment with FLYA. In particular, the peak volume or intensity (2.769E+02) is ''not'' used by the algorithm. | ||
== FLYA scripts == | |||
The CYANA commands to run the automated assignment calculation are stored in two CYANA scripts or "macros". One has the fixed name 'init.cya' and is executed automatically each time CYANA is started. It can also be called any one wants to reinitialize the program. It contains normally at least two commands that read the CYANA library | |||
that defines the residue and experiment types | |||
Revision as of 22:03, 21 July 2013
We want to determine the resonance assignments and the structure of a protein.
Experimental input data
The protein sequence is stored in the file 'demo.seq'.
The following spectra have been measured:
- [1H,13C]-HSQC, called 'C13H1' in FLYA
- [1H,15N]-HSQC, called 'N15H1' in FLYA
- HNCA
- HN(CO)CA, called 'HN_CO_CA' in FLYA
- HNCO
- HN(CA)CO, called 'HN_CA_CO' in FLYA
- CBCANH
- CBCACONH
- HBHACONH
- HCCH-TOCSY, called 'HCCH24' in FLYA
- HCCH-COSY, called 'HCCH7' in FLYA
- C(CO)NH, called 'C_CO_NH' in FLYA
- HC(CO)NH, called 'HC_CO_NH' in FLYA
Peak lists that have been prepared by automatic peak picking with the program NMRView are stored in files XXX.peaks, where XXX denotes the FLYA spectrum type.
Each peak list starts with a header that defines the experiment type and the order of dimensions. For instance, for HNCA.peaks:
# Number of dimensions 3
#FORMAT xeasy3D
#INAME 1 HN
#INAME 2 C
#INAME 3 N
#SPECTRUM HNCA HN C N
5 6.475 58.033 98.548 1 U 2.769E+02 0.000E+00 e 0 0 0 0
6 6.476 62.123 98.126 1 U 2.571E+01 0.000E+00 e 0 0 0 0
7 6.475 54.017 98.159 1 U 2.547E+01 0.000E+00 e 0 0 0 0
The first line specifies the number of dimensions (3 in this case). The '#SPECTRUM' lines gives the experiment type (HNCA, which refers to the corresponding experiment definition in the CYANA library), followed by an identifier for each dimension of the peak list (HN C N) that specifies which chemical shift is stored in the corresponding dimension of the peak list. Below follows one for every peak. For example, the first peak in the HNCA.peaks list has
- Peak number 5
- HN chemical shift 6.475
- C (CA) chemical shift 58.033
- N chemical shift 98.548
The other data are irrelevant for automated chemical shift assignment with FLYA. In particular, the peak volume or intensity (2.769E+02) is not used by the algorithm.
FLYA scripts
The CYANA commands to run the automated assignment calculation are stored in two CYANA scripts or "macros". One has the fixed name 'init.cya' and is executed automatically each time CYANA is started. It can also be called any one wants to reinitialize the program. It contains normally at least two commands that read the CYANA library
that defines the residue and experiment types