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README
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README
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This file explain the folder's structure and files needed to run CSP.
All the framework is "installed" under a folder, this is the CSP_DIR
folder. The source code is in ${CSP_DIR}/src/. The executable is
compiled into ${CSP_DIR}/bin/. The data is in ${CSP_DIR}/data/. And
the scripts to run FREALIGN are in ${CSP_DIR}/frealign/.
To run an experiment a set of files should be properly placed for a
smooth running. This includes the parameter configuration file, data
files and output folders.
Let's say an experiment with the code name exp_name is going to be
run. The .parx file with the initial condition is named
exp_name_1.parx. This file should be in the folder
${CSP_DIR}/data/. The configuration is loaded by CSP reading the file
# ${CSP_DIR}/parameters.config
The ParFile field in this file should be exp_name.parx and is the name
that triggers all the naming convention. [TODO: the extension .parx is
not needed in the parameters.config, fix it.]
The data needed to run an experiment should be, then:
1. Initial parameters:
${CSP_DIR}/data/exp_name_1.parx
2. Image stack:
${CSP_DIR}/data/exp_name_stack.mrc
3. Initial model:
${CSP_DIR}/data/exp_name_1.mrc
Also the WorkingFolder field should be updated, this should be the
${CSP_DIR} folder.
The scripts to run FREALIGN are in the folder ${CSP_DIR}/frealign/. In
particular the FREALIGN configuration file frealign_parameters.
A CSP experiment is run using the script run_csp_experiment.sh from
the ${CSP_DIR} folder.
In order to run FREALIGN only with the particle projections needed
(and increase the speed) a set of stacks/parx files are created. Each
one of this pair corresponds to the set of particle projections in one
of the objects (micrograph or particle). These sets of files are
created (if they do not exist) running the script create_new_stacks.sh.
create_new_stacks.sh saves the files in ${CSP_DIR}/data/exp_name and
they have the following name convention:
# exp_name_TXX_{M,P}YYYY_1.parx
# exp_name_TXX_{M,P}YYYY_stack.mrc
corresponding to the set of particles projections belonging to the
YYYY-th micrograph (M) or particle (P) in the XX-th tilt series
(T). For example GroEL_02_noise_00_T01_M0033_1.parx are the particle
projection of the micrograph 33 in the first tilt series, and
GroEL_02_noise_00_T01_M0033_stack.mrc their images.
run_csp_experiment.sh creates all the links in the
${CSP_DIR}/frealign/ to be used by FREALIGN; this is done before
calling CSP and then removes them.
The output folder is also created by run_csp_experiment.sh in
${CSP_DIR}/frealign/exp_name. Into this folder are going to be copied
all the intermediate files created by FREALIGN everytime it is
called; this could be a lot of files!
FREALIGN is run for evaluating the phase residual (PR) in a particular
point in the CSP manifold. This is done running the script
run_frealign_refine.sh called directly from the CSP executable. This
script is called with only one parameter, the .parx files with the
parameters of the particle projections written by CSP. This file is
saved in ${CSP_DIR}/frealign/exp_name and has the following naming
convention
# exp_name_TXX_{M,P}YYYY_1_ZZZZZZZ.parx
where ZZZZZZZ is the number of times the function GetValue() is called
by Powell in CSP.
Among other tasks run_frealign_refine.sh copies
exp_name_TXX_{M,P}YYYY_1_ZZZZZZZ.parx is copied to
${CSP_DIR}/frealign/ as exp_name_TXX_{M,P}YYYY_1.par and writes the
data_input and raw_images1 fields in the frealign_parameters file with
the correct names (exp_name_TXX_{M,P}YYYY and
exp_name_TXX_{M,P}YYYY_stack). Remember that the files
exp_name_TXX_{M,P}YYYY_stack.mrc and exp_name_TXX_{M,P}YYYY_1.mrc were
linked previously by run_csp_experiment.sh. Also the MASK is set to
0,0,0,1,1.
FREALIGN outputs files in ${CSP_DIR}/frealign/{scratch,log} that are
copied to ${CSP_DIR}/frealign/exp_name, in particular the _2.par
output .par file and the _2_msearch_n.log
After refining all the objects the reconstruction step is performed by
CSP calling the script run_frealign_reconstruction.sh. This script
makes similar tasks as run_frealign_refine.sh and calls
frealign_ali.sh. The output files (maps, fsc files, etc.) are copied
to the ${CSP_DIR}/frealign/exp_name folder.
### Summary ###
To run an experiment based in the par file BASENAME.parx in
${CSP_DIR}/data/ the following files should be present:
${CSP_DIR}/data/BASENAME.parx
${CSP_DIR}/data/BASENAME_1.mrc :the initial 3D model
${CSP_DIR}/data/BASENAME_stack.mrc :the stack of images
and the configuration files should have:
- ${CSP_DIR}/parameters.config
ParFile BASENAME.parx
Note: The data files are usually a symbolic link to another file in
order to reduce the amount of space needed in the hard drive.