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

From CYANA Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
 
(33 intermediate revisions by the same user not shown)
Line 1: Line 1:
The rho files are used to enter auto-relaxation and I(0) values
[[CYANA Commands|back to complete commands list]]
into the program CYANA. For each spin there is a
line with the following data: residue number, residue name and atom
name, the rho and I(0) value, the flag  -1.0000 is used for keeping the fitted value.




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

back to complete commands list


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