CYANA Command: write upl

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.

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),...,(α_n,β_n) and an upper distance bound b imposes on the structure the condition

$d_{\text{eff}}=\left(\sum _{i=1}^{n}d(\alpha _{i},\beta _{i})^{-6}\right)^{-1/6}\leq b$.

d(α_i,β_i) is the distance between the atoms α_i and β_i.

Note that the "effective distance" d_eff 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".