Content-type: text/html Manpage of checkAlignmentLogs

checkAlignmentLogs

Section: User Commands (1)
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NAME

checkAlignmentLogs - check for potentially invalid search results  

SYNOPSIS

checkAlignmentLogs parameterfile.prm firstLogNum lastLogNum  

DESCRIPTION

Alignment searches can return invalid results if the search range specified is too narrow. This will often be indicated by a search that terminates with a best angle or best shift at the end of the specified range. While alignSubset prints warnings about this for each individual particle, it is typically more convenient to see a summary showing the number and percentage of potentially bad searches over all the particles at a particular iteration. CheckAlignmentLogs scans a specified group of individual alignment logs and produces such a summary. Trivial (null), spherical, and hemi-spherical searches are always considered to be valid (i.e. not at end-of-range) in these statistics.

FirstLogNum and lastLogNum indicate the range of log files to check, and are typically set to include all runs of alignSubset for a particular iteration. When serial averaging is being used, this will be all consecutively numbered log files between adjacent -start or -sync and -sync or -finish logs. When parallel averaging is in effect, it will be the second group of numbered logs for a particular iteration. See the prmParser man page for more details.

When PEET is run from the eTomo GUI, checkAlignmentLogs is automatically invoked prior to running averageAll, with the results appearing near the beginning of each *sync.log and *finish.log files.

parameterFile.prm
The name of the PEET parameter file.
firstLogNum
The number of the first log file to be checked.
lastLogNum
The number of the last log file to be checked.
 

FILES

Sample parameter files are available in $PARTICLE_DIR/templates.  

AUTHOR

John Heumann  

SEE ALSO

PEET(1), prmParser(1), prepareRef(1), mergeEM(1), alignSubset(1), and averageAll(1).


 

Index

NAME
SYNOPSIS
DESCRIPTION
FILES
AUTHOR
SEE ALSO

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Time: 21:10:05 GMT, March 20, 2017