CYANA script: cyanafilter: Difference between revisions
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:;-a: list assigned cross peaks that were not assigned manually | :;-a: list assigned cross peaks that were not assigned manually | ||
:;-A: list assigned cross peaks | :;-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): | ||
== See also == | == See also == |
Revision as of 13:59, 12 August 2009
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):