CYANA script: cyanafilter

Synopsis

cyanafilter [option] file ...

Description

Extracts information from the automatic NOESY assignment (*.noa) files. The cyanafilter shell script filters a NOESY assignment report according to a variety of criteria. Assignment information is printed for the peaks that match the given criteria. NOESY assignment reports are produced by the assign command that is used, for instance, in the combined NOESY assignment and structure calculation strategy implemented in the noeassign macro that yields NOESY assignment report files called 'cycle1.noa', 'cycle2.noa', etc. for each cycle of the calculation.

Options:

-a

list assigned cross peaks that were not assigned manually

-A

list assigned cross peaks

-b atom

list peaks with a (used or unused) assignment possibility to the given atom

-c list compatible peaks -e list peaks with not enough quality -h help -i list incompatible peaks -k atom list peaks assigned to the given atom -l atom list peaks assigned manually to given atom -L level list peaks with all assignment possibilities spanning more than level residues -m list manually assigned peaks -M list manually not assigned peaks -n report only the number of matching peaks -p number list peak(s) with the given number -P file list peaks present in the given automated NOESY assignment file -q quality list peaks with less than the given overall assignment quality -Q quality list peaks with more than the given overall assignment quality -r rank list peaks with manual rankrank -R list peaks for which the manual assignment was not found automatically -s short output; do not report network-anchoring details -S spectrum list peaks from the given spectrum -u list unassigned peaks -v list violated peaks -V violation list peaks with distance restraint violation greater than violation file input CYANA automated NOESY assignment file(s) (.noa)

-a

list additionally assigned cross peaks

-A

list assigned cross peaks

-b atom

list peaks with assignment possibility to given atom

-c

list compatible peaks

-e

list peaks with not enough quality

-h

help

-i

list incompatible peaks

-k atom

list peaks assigned to given atom

-l atom

list peaks assigned manually to given atom

-L level

list peaks with residue index difference |i - j| = level

-m

list manually assigned peaks

-M

list manually not assigned peaks

-n

list only number of peaks

-p peaknr

list peak with given number

-P file

list peak present in the given file

-q quality

list peaks with NOE support quality

-Q quality

list peaks with NOE support quality

-r rank

list peaks with manual rank = rank

-R

list peaks with manual assignment not found

-s

short; do not list network-anchoring details

-S spectrum

list peaks from the given spectrum

-u

list unassigned peaks

-v

list violated peaks

-V viol

list peaks with violation greater than viol

file

input CYANA assignment file (.noa)

See also

• assign
• noeassign