CYANA Command: write upl

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 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".