Auto-relaxation and I(0) values: Difference between revisions

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The upper and lower distance limit files are used to enter distance constraints
[[CYANA Commands|back to complete commands list]]
into the program CYANA. For each distance constraint there is a
line with the following data: residue number, residue name and atom
name of the first and second atom, respectively, the distance limit in Å,
and, optionally, the relative weight of the constraint. The default relative
weight is 1. Relative weights should be positive. The weight of a constraint
in the target function equals the relative weight times the weight ing factor for the corresponding type of constraints.


The rho files are used to enter auto-relaxation (rho) and back-predicted diagonal intensities, I(0) values, into the program CYANA. For each spin there is a line with the following data: residue number, residue name and atom name, rho (in seconds [s]) and the I(0) value; the flag  -1.0000 is used for keeping the fitted value.
all experimental values                                      class 1
The classes of experimental values:
H1N                                                          class 2
H2N                                                          class 3
single H on carbon                                            class 4
methylene not pseudo (chemically equivalent or overlapped)    class 5
methylene pseudo (chemically equivalent or overlapped)        class 6
methyl pseudo                                                class 7
When there are only experimentally fitted values listed:
  # Specifying both auto-relaxation (rho) and I(0)
  # Specifying both auto-relaxation (rho) and I(0)
  # Assignment, auto-relaxation, I(0)
  # Assignment, auto-relaxation, I(0),class
  5    SER  HA      3.7067              752840293.0085
  5    SER  HA      3.7067              752840293.0085           1
  6    LYS  HD2      3.5576            1260683444.4590
  6    LYS  HD2      3.5576            1260683444.4590           1
  6    LYS  QE      2.6034            2487355750.6458
  6    LYS  QE      2.6034            2487355750.6458           1
  7    LEU  H        5.0151              438936421.8380
  7    LEU  H        5.0151              438936421.8380           1
  7    LEU  HA      6.2201              224628629.6022
  7    LEU  HA      6.2201              224628629.6022           1
  7    LEU  HB2      8.2344              164972110.8104
  7    LEU  HB2      8.2344              164972110.8104           1


When there are rho values calculated from mean experimental values per spin-type:
  # Specifying rho only
  # Specifying rho only
  # Assignment, auto-relaxation, I(0))
  # Assignment, auto-relaxation, I(0)),class
  5    SER  HA      3.7067              -1.0000
  5    SER  HA      4.5175                    -1.0000           4
  6    LYS  HD2      3.5576              -1.0000
  6    LYS  HD2      6.8765                    -1.0000           5
  6    LYS  QE      2.6034            -1.0000
  6    LYS  QE      3.8765                    -1.0000           6
  7    LEU  H        5.0151              -1.0000
  7    LEU  H        5.0283                    -1.0000           2
  7    LEU  HA      6.2201              -1.0000
  7    LEU  HA      4.5175                    -1.0000           4
  7    LEU  HB2      8.2344              -1.0000
  7    LEU  HB2      6.8765                    -1.0000           5


For generic normalize eNOEs, there are rho and izero values from mean experimental values per spin-type:
  # Specifying I(0) only
  # Specifying I(0) only
  # Assignment, auto-relaxation, I(0)
  # Assignment, auto-relaxation, I(0),class
  5    SER  HA      -1.0000             752840293.0085
  5    SER  HA      4.5175                    229069008.0000           4
  6    LYS  HD2      -1.0000             1260683444.4590
  6    LYS  HD2      6.8765                    147877728.0000           5
  6    LYS  QE      -1.0000            2487355750.6458
  6    LYS  QE      3.8765                    1747547361.4181          6
  7    LEU  H        -1.0000             438936421.8380
  7    LEU  H        5.0283                    292925280.0000           2
  7    LEU  HA      -1.0000             224628629.6022
  7    LEU  HA      4.5175                    229069008.0000           4
  7    LEU  HB2      -1.0000             164972110.8104
  7    LEU  HB2      6.8765                    147877728.0000           5

Latest revision as of 17:48, 29 May 2019

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The rho files are used to enter auto-relaxation (rho) and back-predicted diagonal intensities, I(0) values, into the program CYANA. For each spin there is a line with the following data: residue number, residue name and atom name, rho (in seconds [s]) and the I(0) value; the flag -1.0000 is used for keeping the fitted value. 

all experimental values                                       class 1

The classes of experimental values:
H1N                                                           class 2
H2N                                                           class 3
single H on carbon                                            class 4
methylene not pseudo (chemically equivalent or overlapped)    class 5
methylene pseudo (chemically equivalent or overlapped)        class 6
methyl pseudo                                                 class 7



When there are only experimentally fitted values listed: 

# Specifying both auto-relaxation (rho) and I(0)
# Assignment, auto-relaxation, I(0),class
5    SER  HA       3.7067              752840293.0085           1
6    LYS  HD2      3.5576             1260683444.4590           1
6    LYS  QE       2.6034             2487355750.6458           1
7    LEU  H        5.0151              438936421.8380           1
7    LEU  HA       6.2201              224628629.6022           1
7    LEU  HB2      8.2344              164972110.8104           1

When there are rho values calculated from mean experimental values per spin-type: 

# Specifying rho only
# Assignment, auto-relaxation, I(0)),class
5    SER  HA       4.5175                     -1.0000           4
6    LYS  HD2      6.8765                     -1.0000           5
6    LYS  QE       3.8765                     -1.0000           6
7    LEU  H        5.0283                     -1.0000           2
7    LEU  HA       4.5175                     -1.0000           4
7    LEU  HB2      6.8765                     -1.0000           5

For generic normalize eNOEs, there are rho and izero values from mean experimental values per spin-type: 

# Specifying I(0) only
# Assignment, auto-relaxation, I(0),class
5    SER  HA       4.5175                    229069008.0000           4
6    LYS  HD2      6.8765                    147877728.0000           5
6    LYS  QE       3.8765                    1747547361.4181          6
7    LEU  H        5.0283                    292925280.0000           2
7    LEU  HA       4.5175                    229069008.0000           4
7    LEU  HB2      6.8765                    147877728.0000           5
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