CYANA Command: write upl: Difference between revisions
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== Parameters == | == Parameters == | ||
; file=''filename''.upl | ; file=''filename''.upl:(required) | ||
:( | ;list=''integer'':(default: 1) | ||
; sorted | ;nmrstar=''integer'':(default: 2) | ||
;details | |||
; swapped | ;multiple | ||
;sorted | |||
; xplor | ;swapped | ||
;xplor | |||
; nocomments | ;nocomments | ||
;append | |||
; append | |||
== Description == | == Description == | ||
Writes | Writes an upper limit distance restraint file. Optionally, the output may be appended to an existing file. | ||
==== Ambiguous distance restraints ==== | |||
Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition | Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with ''n'' assignments to atom pairs (''α''<sub>1</sub>,''β''<sub>1</sub>),...,(''α<sub>n</sub>'',''β<sub>n</sub>'') and an upper distance bound ''b'' imposes on the structure the condition | ||
<math>d_{eff} = \(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\)^{-1/6} \le b</math>. | :<math>d_\text{eff} = \left(\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6}\right)^{-1/6} \le b</math>. | ||
''d''(''α''<sub>i</sub>,''β''<sub>i</sub>) is the distance between the atoms ''α''<sub>i</sub> and ''β''<sub>i</sub>. | |||
Note that the "effective distance" ''d''<sub>eff</sub> cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound ''b'', regardless of the possible presence of other assignments that correspond to longer distances. | |||
==== Shorthand form ==== | |||
Instead of the command | Instead of the command | ||
Latest revision as of 11:11, 12 January 2010
Write upper distance limit file
Parameters
- file=filename.upl
- (required)
- list=integer
- (default: 1)
- nmrstar=integer
- (default: 2)
- details
- multiple
- sorted
- swapped
- xplor
- nocomments
- append
Description
Writes an upper limit distance restraint file. Optionally, the output may be appended to an existing file.
Ambiguous distance restraints
Distance restraints can either be unambiguous i.e. assigned to a single pair of atoms, or ambiguous, i.e. assigned to multiple pairs of atoms. In the input file, an ambiguous distance restraint is composed of several lines. The first line of an ambiguous distance restraint specifies the first assignment and the upper distance bound, as in the case of an unambiguous distance restraint. The following lines specify additional assignments with an upper distance bound of zero. An ambiguous distance restraint with n assignments to atom pairs (α1,β1),...,(αn,βn) and an upper distance bound b imposes on the structure the condition
- .
d(αi,βi) is the distance between the atoms αi and βi.
Note that the "effective distance" deff cannot be longer than the shortest of the individual distances. Therefore, an ambiguous distance restraint is fulfilled if at least one of the assignments corresponds to a distance that does not exceed the upper bound b, regardless of the possible presence of other assignments that correspond to longer distances.
Shorthand form
Instead of the command
write upl filename.upl
the shorthand version
write filename.upl
can be used if the filename extension is ".upl".