CYANA script: cyanatable: Difference between revisions

From CYANA Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
== Synopsis ==
== Synopsis ==


'''cyanatable [''option''] [''prefix''] [''logfile'']'''
== Description ==
 
The '''cyanatable''' shell script produces a summary table of a combined
automated NOESY assignment and structure calculation run executed with
the '''noeassign''' macro. Statistics on the NOESY peak assignments, the
upper distance bounds, and the structure calculation are extracted from
output files produced by '''noeassign''' and arranged in a table with one
column for each cycle of combined automated NOESY assignment and
structure calculation. The standard output from the '''noeassign''' run must
have been collected in a log file called AUTO.out, CANDID.out, CALC.out,
''prefix''.out, or ''logfile''.
 
If present, the given ''prefix'' is prepended to all other input file
names. If, for instance, ''prefix'' is '''run1''', then the '''cyanatable'''
script will look for files named '''run1cycle1.noa''', '''run1cycle1.ovw''' etc.
instead of the files with default file names '''cycle1.noa''', '''cycle1.ovw'''
etc.
 
This command can be invoked from the Unix shell or from within CYANA.
The command syntax follows Unix (not INCLAN) conventions.


Produces a summary table of a combined automated NOESY assignment and structure calculation run executed with the [[CYANA Macro: noeassign|'''noeassign''']] macro. The '''cyanatable''' command can be used for complete or partially completed runs. Statistics on the NOESY peak assignments, the upper distance bounds, and the structure calculation are extracted from output files produced by [[CYANA Macro: noeassign|'''noeassign''']] and arranged in a table with one column for each cycle of combined automated NOESY assignment and structure calculation. The standard output from the [[CYANA Macro: noeassign|'''noeassign''']] run must have been collected in a log file called either '''AUTO.out''', '''CALC.out''', '''CANDID.out''', ''prefix'''''.out''', or ''logfile''.
If present, the given ''prefix'' is prepended to all other input file names. For instance, if the prefix is '''run1''', then the '''cyanatable''' script will look for files named '''run1cycle1.noa''', '''run1cycle1.ovw''' etc. instead of the files with default file names '''cycle1.noa''',''' cycle1.ovw''' etc.
Options:
Options:
 
:;-h: help
;-h: help
:;-l: long, more detailed output
;-l: long, more detailed output
:;-p: report percentages instead of absolute values
;-p: report percentages instead of absolute values


== See also ==
== See also ==


* [[CYANA Macro: noeassign|noeassign]]
* [[CYANA Macro: noeassign|noeassign]]

Latest revision as of 14:19, 12 August 2009

Synopsis

Description

Produces a summary table of a combined automated NOESY assignment and structure calculation run executed with the noeassign macro. The cyanatable command can be used for complete or partially completed runs. Statistics on the NOESY peak assignments, the upper distance bounds, and the structure calculation are extracted from output files produced by noeassign and arranged in a table with one column for each cycle of combined automated NOESY assignment and structure calculation. The standard output from the noeassign run must have been collected in a log file called either AUTO.out, CALC.out, CANDID.out, prefix.out, or logfile. If present, the given prefix is prepended to all other input file names. For instance, if the prefix is run1, then the cyanatable script will look for files named run1cycle1.noa, run1cycle1.ovw etc. instead of the files with default file names cycle1.noa, cycle1.ovw etc. Options:

-h
help
-l
long, more detailed output
-p
report percentages instead of absolute values

See also

Retrieved from "https://cyana.org/w/index.php?title=CYANA_script:_cyanatable&oldid=6984"