Manpage of checkAlignmentLogs
Section: User Commands (1)
Return to Main Contents
checkAlignmentLogs - check for potentially invalid search results
checkAlignmentLogs parameterfile.prm firstLogNum lastLogNum
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.
The name of the PEET parameter file.
The number of the first log file to be checked.
The number of the last log file to be checked.
Sample parameter files are available in $PARTICLE_DIR/templates.
PEET(1), prmParser(1), prepareRef(1), mergeEM(1), alignSubset(1),
- SEE ALSO
This document was created by
using the manual pages.
Time: 18:16:05 GMT, January 11, 2021