CYANA Command: write upl: Difference between revisions
No edit summary |
|||
| Line 22: | Line 22: | ||
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} = | <math>d_{eff} = (\sum_{i=1}^n d(\alpha_i,\beta_i)^{-6})^{-1/6} \le b</math>. | ||
Revision as of 23:38, 5 February 2009
Write upper distance limit file
Parameters
- file=filename.upl
- (required) The name of the output upper distance limit file. The default filename extension ".upl" is used unless a filename extension is given explicitly.
- sorted
- Option to sort the distance restraints by the first and second atom. By default, the distance restraints are written in the order in which they are stored in the program, e.g. the order in which they have been read from an input file.
- swapped
- Option to output restraints that involve diastereotopic hydrogens or methyl groups after optimal swapping of the stereopartners for minimal target function value.
- xplor
- Option to output the file in the format of the program XPLOR instead of the standard distance restraint file format of the program CYANA.
- nocomments
- Option to suppress the output of comments such as the number of the peak from which the restraint originated.
- append
- Option to append the output to the given file. By default, an already existing output file is overwritten.
Description
Writes a file with the currently selected upper distance limits in the standard distance restraint file format of the program CYANA, or optionally in XPLOR format.
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
.
Instead of the command
write upl filename.upl
the shorthand version
write filename.upl
can be used if the filename extension is ".upl".