In
addition to the interactive operation mode (the GUI mode) described in
the previous sections, micrograph images can also be processed under a
standing alone computing mode (the COM mode), in which scoring maps
required by the algorithmic particle selection are calculated but not
screened. These maps can later be read into the system under the GUI
mode for interactive particle selection. The COM mode enables
batch-processing that can greatly enhance productivity through
scripting and distributed computing. To start the program under this
mode at a shell command-line, type the command and filename
signature
project_file.prj
The project file for each micrograph can be created as follows:
- Define a new project space (from Menu
: Project : New).
- Load one micrograph image (from Menu : Data :
Micrograph : Load MRC) and set
proper pixel size.
- Inspect the quality of the micrograph and mask out defects.
- Load template images (from Menu : Data : Template
: Load MRC)
and set proper rotational search parameters.
- Define particle parameters (in Particle
OpPanel).
- Save the project definition for this micrograph (from Menu
: Project : Save).
- Load another micrograph and repeat the procedure, starting
from step 2.
- When done, close the project space (from Menu
: Project : Close).
Once the project files have been created for all the micrographs to be
screened, batching processing can be commenced by using the C-shell
script listed below. It is assumed that the micrographs are numerically
named with MRC extension (e.g., "1234.mrc"). When multiple
computing
nodes are available, the
micrographs can be divided into a number of groups. One task script can
be created for each group and submitted to a separate node.
#!/bin/csh
#
#
SIGNATURE batch processing script
# the
first micrograph ID
set
FIRST_FILM=1000
# the
last micrograph ID
set
LAST_FILM=9999
# the
"screening/" directory in your project-space
set
PROJ_ROOT=".../your_project.ems/screening"
#
location of Signature
executable
set
EXEC_CODE=".../bin_directory/signature"
#
AUTOMATIC SCREENING STARTS
set
this_film=$FIRST_FILM
while (
$this_film <= $LAST_FILM )
set THIS_PROJ="${PROJ_ROOT}/${this_film}.prj"
set LOG_FILE="${PROJ_ROOT}/${this_film}.log"
if ( -e ${THIS_PROJ} ) then
echo "Screening micrograph $this_film ..."
${EXEC_CODE}
${THIS_PROJ} >& ${LOG_FILE}
endif
@ this_film++
end
# END
A log file (e.g., "1234.log")
will be created for each screening
project. There should be
no error message in the log file for a successfully accomplished task.
A quick check can be done by, for example,
grep
-i "err" 1234.log
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