From 224d1784ab57e58ce34f3227004c536bc326422c Mon Sep 17 00:00:00 2001
From: Huabin Zhou <huabin.zhou@utsouthwestern.edu>
Date: Mon, 14 Apr 2025 11:00:14 -0500
Subject: [PATCH] Update the contour level control
---
README.md | 4 +-
src/catm.egg-info/PKG-INFO | 106 +-
src/catm.egg-info/SOURCES.txt | 17 +-
src/catm.egg-info/entry_points.txt | 1 +
src/catm.egg-info/requires.txt | 11 +-
src/catm.egg-info/top_level.txt | 14 +-
src/config.py | 2 +-
src/file_handler.py | 23 +-
test/s210/tm/config.py | 2 +-
test/s68/catm/config.py | 2 +-
test/s68/catm/results/match_raw_results.xml | 6400 ++++++++---------
test/s68/catm/results/s68.test1.catm.coords | 16 +-
test/s68/catm/results/s68.test1.catm.csv | 16 +-
.../catm/results/s68.test1.catm.models.mrc | Bin 257024 -> 257024 bytes
test/s68/catm/results/s68.test1.catm.star | 19 +-
test/s68/catm/results/s68.test1.catm.xml | 16 +-
test/s68/tm/config.py | 2 +-
17 files changed, 3389 insertions(+), 3262 deletions(-)
diff --git a/README.md b/README.md
index 415672f..3d9e61a 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ git clone https://git.biohpc.swmed.edu/s194231/CATM.git #(optional if you alread
cd CATM
```
-3. Install the package, if you want to develop base on this software, add -dev option
+3. Install the package, if you want to develop base on this software, add -e option
```
pip install .
@@ -59,6 +59,8 @@ Please refer to the Tutorial file for step-by-step instructions on testing the i
### 2. Determine the contour level for template matching and clash resolver
- Run the counter_level_check.py file to determine the contour level for your template. This step only needs to be done once for similar datasets.
+- Now, you might skip this step, if you leave the contour_level empty, the program will do the job for you
+- You might still need to give a proper "shrinkage_factor" parameter for the clash resolver
```
python counter_level_check.py path_to_template.mrc [ctf_model or missing wedge info]
```
diff --git a/src/catm.egg-info/PKG-INFO b/src/catm.egg-info/PKG-INFO
index 7695a24..33aff20 100644
--- a/src/catm.egg-info/PKG-INFO
+++ b/src/catm.egg-info/PKG-INFO
@@ -1,7 +1,7 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
Name: catm
-Version: 0.0.0
-Summary: A software for template matching and clash resolving in cryo-EM
+Version: 0.1.0
+Summary: A software for template matching and clash resolving in cryo-ET
Author-email: Huabin Zhou <huabin.zhou@utsouthwestern.edu>
License: Copyright (c) 2024 The University of Texas Southwestern Medical Center.
@@ -27,10 +27,8 @@ Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
-Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Cryo-EM Data Processing
Classifier: Operating System :: OS Independent
-Classifier: Framework :: Matplotlib
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE.md
@@ -40,19 +38,26 @@ Requires-Dist: mrcfile
Requires-Dist: scikit-learn
Requires-Dist: scipy
Requires-Dist: lxml
+Requires-Dist: starfile
+Requires-Dist: tqdm
+Requires-Dist: matplotlib
Provides-Extra: stats
Requires-Dist: scipy>=1.7; extra == "stats"
Requires-Dist: statsmodels>=0.12; extra == "stats"
Provides-Extra: dev
-Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: vg; extra == "dev"
+Requires-Dist: networkx; extra == "dev"
+Requires-Dist: black; extra == "dev"
Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pycm; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: pytest-xdist; extra == "dev"
-Requires-Dist: flake8; extra == "dev"
Requires-Dist: mypy; extra == "dev"
Requires-Dist: pandas-stubs; extra == "dev"
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: flit; extra == "dev"
+Requires-Dist: mpld3; extra == "dev"
+Requires-Dist: jupyter; extra == "dev"
Provides-Extra: docs
Requires-Dist: numpydoc; extra == "docs"
Requires-Dist: nbconvert; extra == "docs"
@@ -63,3 +68,90 @@ Requires-Dist: sphinx-issues; extra == "docs"
Requires-Dist: sphinx-design; extra == "docs"
Requires-Dist: pyyaml; extra == "docs"
Requires-Dist: pydata_sphinx_theme==0.10.0rc2; extra == "docs"
+Dynamic: license-file
+
+# Context Aware Template Matching (CATM) for Cryo-ET data analysis
+
+# CATM version 0.1
+
+## Introduction
+
+This software is designed to assign models in crowded cryo-ET tomograms. Its primary function is to take pre-picked coordinates
+from other software as input and calculate the local cross-correlation coefficients (CCCs) with the provided templates.
+The software then integrates this information with geometric constraints between models to achieve highly accurate assignments.
+It also includes a clash resolver module to optimize the poses of models, with support for multi-template assignments.
+
+## Installation
+
+Python version 3.5 or higher is required. It is recommended to create a separate environment for installation to
+avoid conflicts with other packages. The installation typically takes less than 5 minutes, depending on your network
+speed and hardware performance.
+
+
+1. Creat a new vitual enviroment (optional)
+
+```
+conda create -n CATM python==3.10
+```
+
+2. Download the package from gitlab and change directory to the CATM folder
+
+```
+git clone https://git.biohpc.swmed.edu/s194231/CATM.git #(optional if you already have the files)
+cd CATM
+```
+
+3. Install the package, if you want to develop base on this software, add -e option
+
+```
+pip install .
+```
+4. After installation, activate the conda environment if not yet
+```
+conda activate CATM
+```
+
+## Test the installation and Tutorial
+
+Please refer to the Tutorial file for step-by-step instructions on testing the installation and using the software.
+
+
+
+## General Usage
+
+- The program currently supports three modes: "CATM", "CATM-local", and "general TM".
+
+### 1. Prepare your data, required files are:
+
+- A tomogram file in .mrc format, typically produced by back-projection and low-pass filtered.
+- A list of candidate particles from deep-learning-based pickers, manual picking, or other methods. Supported formats include .csv, .coord, and .star.
+- A 3D CTF model from Warp or Relion (optional). If not provided, you must specify the missing wedge information.
+- One or more template files in cubic volume format.
+- Corresponding mask files for each template (optional). These must have the same dimensions as the templates. If not provided, a tight mask will be generated automatically (recommended).
+### 2. Determine the contour level for template matching and clash resolver
+
+- Run the counter_level_check.py file to determine the contour level for your template. This step only needs to be done once for similar datasets.
+```
+ python counter_level_check.py path_to_template.mrc [ctf_model or missing wedge info]
+ ```
+- Examine the contour level in Chimera/ChimeraX and choose the one with the least artifacts.
+
+
+### 3.Copy the config.py file to your working directory and adjust the parameters
+
+- The key parameters should be adjusted according to your needs. The program supports three modes: "CATM", "CATM-local", and "TM".
+-
+
+### 4. Run the program and analyze the results
+
+```
+CATM
+```
+
+Run the program in your working directory. The program will output results in .csv, .coord, and .star formats. A back-mapped tomogram will also be generated.
+
+## License
+
+UTSW open source
+
+**Free Software for academia!**
diff --git a/src/catm.egg-info/SOURCES.txt b/src/catm.egg-info/SOURCES.txt
index 48df523..7fef464 100644
--- a/src/catm.egg-info/SOURCES.txt
+++ b/src/catm.egg-info/SOURCES.txt
@@ -1,22 +1,25 @@
LICENSE.md
README.md
pyproject.toml
-src/basic.py
src/catm.py
src/clash_resolver.py
src/config.py
+src/config_loader.py
src/file_handler.py
-src/old_utils.py
-src/run.py
+src/filter_tomograms.py
+src/geo_utils.py
+src/global_template_matching.py
+src/global_template_matching_chunk.py
+src/misc.py
+src/plot_nucleosome_with_z.py
src/template_matching.py
+src/test_ccc.py
src/test_config.py
+src/test_multiprocessing.py
src/utils.py
src/catm.egg-info/PKG-INFO
src/catm.egg-info/SOURCES.txt
src/catm.egg-info/dependency_links.txt
src/catm.egg-info/entry_points.txt
src/catm.egg-info/requires.txt
-src/catm.egg-info/top_level.txt
-src/misc/angluar_assement.py
-src/templates/generate_spherical_mask.py
-src/templates/rotate_tomo.py
\ No newline at end of file
+src/catm.egg-info/top_level.txt
\ No newline at end of file
diff --git a/src/catm.egg-info/entry_points.txt b/src/catm.egg-info/entry_points.txt
index 00fe888..e69f286 100644
--- a/src/catm.egg-info/entry_points.txt
+++ b/src/catm.egg-info/entry_points.txt
@@ -1,2 +1,3 @@
[console_scripts]
catm = catm:main
+tm = catm:main
diff --git a/src/catm.egg-info/requires.txt b/src/catm.egg-info/requires.txt
index 3568fc1..9c8c1d0 100644
--- a/src/catm.egg-info/requires.txt
+++ b/src/catm.egg-info/requires.txt
@@ -4,17 +4,24 @@ mrcfile
scikit-learn
scipy
lxml
+starfile
+tqdm
+matplotlib
[dev]
-matplotlib
+vg
+networkx
+black
pytest
+pycm
pytest-cov
pytest-xdist
-flake8
mypy
pandas-stubs
pre-commit
flit
+mpld3
+jupyter
[docs]
numpydoc
diff --git a/src/catm.egg-info/top_level.txt b/src/catm.egg-info/top_level.txt
index da01f31..7774382 100644
--- a/src/catm.egg-info/top_level.txt
+++ b/src/catm.egg-info/top_level.txt
@@ -1,14 +1,16 @@
-basic
catm
clash_resolver
config
-csv
+config_loader
file_handler
+filter_tomograms
+geo_utils
+global_template_matching
+global_template_matching_chunk
misc
-old_utils
-results
-run
+plot_nucleosome_with_z
template_matching
-templates
+test_ccc
test_config
+test_multiprocessing
utils
diff --git a/src/config.py b/src/config.py
index 5585e2c..2064256 100644
--- a/src/config.py
+++ b/src/config.py
@@ -22,7 +22,7 @@ tomogram = input_folder + tomoID + ".test1.lps25.mrc"
black_on_white = 1 # The contrast of tomogram, 0 if the particle has white contrast (positive values)
templates = [input_folder + "mono-8Apx-lps30-box30-rot12-core.mrc"]
-contour_level = [0.2]
+contour_level = [0.2] # Level it empty if you can't decide, we could calculate it internally
# Masks are required to be the same shape as the templates
# One can create the mask in Relion with soft edges, extend 2 and soft 3 is recommended
masks = [
diff --git a/src/file_handler.py b/src/file_handler.py
index 6441edb..f00285c 100644
--- a/src/file_handler.py
+++ b/src/file_handler.py
@@ -6,7 +6,7 @@ from lxml import etree
import os
import importlib.util
import starfile
-
+from utils import apply_ctf, apply_wedge, prepare_ctf_volumes
def read_mrc(filename):
with mrcfile.open(filename) as mrc:
@@ -178,6 +178,25 @@ def parse_input():
else:
print("No CTF model found! Will use missing wedge compensation only!")
ctf_model = None
+ #determine the contour_level
+ if user_inputs["contour_level"]:
+ contour_level = user_inputs["contour_level"]
+ else:
+ contour_level = []
+ for i in range (len(templates)):
+ if user_inputs["ctf_model_file"]:
+ ctf = prepare_ctf_volumes(ctf_model[i], templates[i])
+ temp = apply_ctf(templates[i], ctf)
+ else:
+ temp = apply_wedge(templates[i], user_inputs["missing_wedge"])
+ # Flatten the array to 1D
+ flattened = temp.flatten()
+ # Optionally, remove background/zeros if needed
+ nonzero_values = flattened[flattened > 0]
+ # Compute the 90th percentile cutoff
+ cutoff = np.percentile(nonzero_values, 90)
+ contour_level.append(cutoff)
+ print("No contour level specified, used ", contour_level)
# read the coordinate file
if config.testTM:
@@ -225,7 +244,7 @@ def parse_input():
return {
"tomogram": tomogram,
"templates": templates,
- "contour_level": user_inputs["contour_level"],
+ "contour_level": contour_level, #user_inputs["contour_level"],
"masks": masks,
"coords": coords,
"ctf_model": ctf_model,
diff --git a/test/s210/tm/config.py b/test/s210/tm/config.py
index 046548b..768b0eb 100644
--- a/test/s210/tm/config.py
+++ b/test/s210/tm/config.py
@@ -22,7 +22,7 @@ tomogram = input_folder + tomoID + ".test1.lps25.mrc"
black_on_white = 1 # The contrast of tomogram, 0 if the particle has white contrast (positive values)
templates = [input_folder + "mono-8Apx-lps30-box30-rot12-core.mrc"]
-contour_level = [0.2]
+contour_level = [0.2]# Level it empty if you can't decide, we could calculate it internally
# Masks are required to be the same shape as the templates
# One can create the mask in Relion with soft edges, extend 2 and soft 3 is recommended
masks = [
diff --git a/test/s68/catm/config.py b/test/s68/catm/config.py
index 843fceb..ce9a09a 100644
--- a/test/s68/catm/config.py
+++ b/test/s68/catm/config.py
@@ -21,7 +21,7 @@ input_folder = "inputs/"
tomogram = input_folder + tomoID + ".test1.lps25.mrc"
black_on_white = 1 # The contrast of tomogram, 0 if the particle has white contrast (positive values)
templates = [input_folder + "mono-8Apx-lps30-box30-rot12-core.mrc"]
-contour_level = [0.2]
+contour_level = None #[0.2]# Level it empty if you can't decide, we could calculate it internally
# Masks are required to be the same shape as the templates
# One can create the mask in Relion with soft edges, extend 2 and soft 3 is recommended
masks = [
diff --git a/test/s68/catm/results/match_raw_results.xml b/test/s68/catm/results/match_raw_results.xml
index 92b8149..0038b92 100644
--- a/test/s68/catm/results/match_raw_results.xml
+++ b/test/s68/catm/results/match_raw_results.xml
@@ -1,3218 +1,3218 @@
<objlist>
<subtomo>
- <object subtomo_idx="0" x="23" y="18" z="14" phi="-173" theta="108" psi="33" CCC="0.549446" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="13" phi="-173" theta="108" psi="33" CCC="0.547403" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="16" phi="15" theta="92" psi="26" CCC="0.543960" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="15" phi="15" theta="92" psi="26" CCC="0.540403" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="16" phi="18" theta="92" psi="26" CCC="0.536966" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="13" phi="-176" theta="94" psi="37" CCC="0.534427" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="14" phi="-176" theta="94" psi="37" CCC="0.532497" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="15" phi="18" theta="92" psi="26" CCC="0.532226" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="15" phi="15" theta="92" psi="26" CCC="0.530206" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="16" phi="15" theta="92" psi="26" CCC="0.525735" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="18" z="15" phi="15" theta="92" psi="26" CCC="0.520483" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="15" phi="18" theta="92" psi="26" CCC="0.519953" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="15" phi="-161" theta="115" psi="36" CCC="0.517877" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="15" phi="0" theta="103" psi="43" CCC="0.517534" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="16" phi="5" theta="97" psi="13" CCC="0.517429" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="15" phi="-155" theta="111" psi="36" CCC="0.516181" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="14" phi="-155" theta="111" psi="36" CCC="0.516115" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="15" phi="7" theta="96" psi="40" CCC="0.516008" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="12" phi="-173" theta="108" psi="33" CCC="0.515931" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="14" phi="-161" theta="115" psi="36" CCC="0.515827" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="15" phi="-173" theta="108" psi="33" CCC="0.515576" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="17" phi="15" theta="92" psi="26" CCC="0.514077" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="15" phi="5" theta="97" psi="13" CCC="0.512866" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="16" phi="10" theta="81" psi="50" CCC="0.511469" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="16" phi="18" theta="92" psi="26" CCC="0.511342" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="14" phi="-173" theta="108" psi="33" CCC="0.511177" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="15" phi="-161" theta="115" psi="36" CCC="0.510788" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="14" phi="179" theta="90" psi="14" CCC="0.510349" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="15" phi="10" theta="81" psi="50" CCC="0.510013" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="14" phi="-176" theta="94" psi="37" CCC="0.509834" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="18" z="15" phi="18" theta="92" psi="26" CCC="0.509619" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="14" phi="0" theta="103" psi="43" CCC="0.509601" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="17" phi="18" theta="92" psi="26" CCC="0.507989" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="13" phi="179" theta="90" psi="14" CCC="0.507983" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="12" phi="-176" theta="94" psi="37" CCC="0.507309" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="14" phi="15" theta="92" psi="26" CCC="0.506992" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="16" phi="7" theta="96" psi="40" CCC="0.506855" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="14" phi="15" theta="92" psi="26" CCC="0.506821" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="13" phi="-176" theta="94" psi="37" CCC="0.504293" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="18" z="16" phi="15" theta="92" psi="26" CCC="0.504177" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="18" z="14" phi="15" theta="92" psi="26" CCC="0.502741" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="14" phi="18" theta="92" psi="26" CCC="0.501055" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="15" phi="-176" theta="94" psi="37" CCC="0.499221" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="14" phi="18" theta="92" psi="26" CCC="0.496118" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="13" phi="-173" theta="108" psi="33" CCC="0.495435" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="16" phi="0" theta="103" psi="43" CCC="0.494825" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="16" phi="-161" theta="115" psi="36" CCC="0.494085" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="20" z="16" phi="15" theta="92" psi="26" CCC="0.492899" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="18" z="14" phi="18" theta="92" psi="26" CCC="0.492621" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="17" phi="5" theta="97" psi="13" CCC="0.492270" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="15" phi="2" theta="81" psi="41" CCC="0.491720" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="14" phi="7" theta="96" psi="40" CCC="0.491699" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="19" z="17" phi="15" theta="92" psi="26" CCC="0.491149" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="18" z="16" phi="18" theta="92" psi="26" CCC="0.490900" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="16" phi="2" theta="81" psi="41" CCC="0.490108" model="0.000000"/>
- <object subtomo_idx="0" x="22" y="19" z="14" phi="10" theta="81" psi="50" CCC="0.489373" model="0.000000"/>
- <object subtomo_idx="0" x="23" y="18" z="12" phi="175" theta="113" psi="17" CCC="0.488410" model="0.000000"/>
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diff --git a/test/s68/catm/results/s68.test1.catm.coords b/test/s68/catm/results/s68.test1.catm.coords
index fe6d511..cc13c58 100644
--- a/test/s68/catm/results/s68.test1.catm.coords
+++ b/test/s68/catm/results/s68.test1.catm.coords
@@ -1,8 +1,8 @@
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diff --git a/test/s68/catm/results/s68.test1.catm.csv b/test/s68/catm/results/s68.test1.catm.csv
index 8d4502e..c9441df 100644
--- a/test/s68/catm/results/s68.test1.catm.csv
+++ b/test/s68/catm/results/s68.test1.catm.csv
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diff --git a/test/s68/catm/results/s68.test1.catm.star b/test/s68/catm/results/s68.test1.catm.star
index 0ca0fe9..35b8bde 100644
--- a/test/s68/catm/results/s68.test1.catm.star
+++ b/test/s68/catm/results/s68.test1.catm.star
@@ -1,4 +1,4 @@
-# Created by the starfile Python package (version 0.5.1) at 05:19:40 on 11/10/2024
+# Created by the starfile Python package (version 0.5.8) at 10:53:32 on 14/04/2025
data_
@@ -11,13 +11,14 @@ _rlnAngleRot #4
_rlnAngleTilt #5
_rlnAnglePsi #6
_ccc #7
-23 18 14 97.000000 108.000000 123.000000 0.549446
-24 33 20 -58.000000 145.000000 -124.000000 0.524169
-18 7 23 91.000000 147.000000 -27.000000 0.460670
-12 32 32 137.000000 111.000000 59.000000 0.498119
-30 15 5 -102.000000 76.000000 179.000000 0.453616
-33 34 20 154.000000 79.000000 -50.000000 0.428498
-17 35 7 -42.000000 83.000000 -148.000000 0.416486
-18 20 23 99.000000 105.000000 -11.000000 0.430668
+_rlnTomoName #8
+23 18 14 105.000000 93.000000 131.000000 0.600476 s68
+23 33 19 124.000000 158.000000 -132.000000 0.552363 s68
+10 32 33 -41.000000 112.000000 49.000000 0.516575 s68
+17 7 25 -35.000000 63.000000 73.000000 0.471530 s68
+33 34 19 168.000000 87.000000 -62.000000 0.452047 s68
+30 15 5 -96.000000 82.000000 -162.000000 0.498885 s68
+18 20 24 70.000000 81.000000 -13.000000 0.475971 s68
+16 33 7 142.000000 96.000000 -154.000000 0.458083 s68
diff --git a/test/s68/catm/results/s68.test1.catm.xml b/test/s68/catm/results/s68.test1.catm.xml
index c29ad49..101bfcc 100644
--- a/test/s68/catm/results/s68.test1.catm.xml
+++ b/test/s68/catm/results/s68.test1.catm.xml
@@ -1,26 +1,26 @@
<objlist>
<subtomo>
- <object subtomo_idx="0" x="23" y="18" z="14" phi="-173" theta="108" psi="33" CCC="0.549446" model="0.000000"/>
+ <object subtomo_idx="0" x="23" y="18" z="14" phi="-165" theta="93" psi="41" CCC="0.600476" model="0.000000"/>
</subtomo>
<subtomo>
- <object subtomo_idx="1" x="24" y="33" z="20" phi="32" theta="145" psi="146" CCC="0.524169" model="0.000000"/>
+ <object subtomo_idx="1" x="23" y="33" z="19" phi="-146" theta="158" psi="138" CCC="0.552363" model="0.000000"/>
</subtomo>
<subtomo>
- <object subtomo_idx="2" x="18" y="7" z="23" phi="-179" theta="147" psi="-117" CCC="0.460670" model="0.000000"/>
+ <object subtomo_idx="2" x="10" y="32" z="33" phi="49" theta="112" psi="-41" CCC="0.516575" model="0.000000"/>
</subtomo>
<subtomo>
- <object subtomo_idx="3" x="12" y="32" z="32" phi="-133" theta="111" psi="-31" CCC="0.498119" model="0.000000"/>
+ <object subtomo_idx="3" x="17" y="7" z="25" phi="55" theta="63" psi="-17" CCC="0.471530" model="0.000000"/>
</subtomo>
<subtomo>
- <object subtomo_idx="4" x="30" y="15" z="5" phi="-12" theta="76" psi="89" CCC="0.453616" model="0.000000"/>
+ <object subtomo_idx="4" x="33" y="34" z="19" phi="-102" theta="87" psi="-152" CCC="0.452047" model="0.000000"/>
</subtomo>
<subtomo>
- <object subtomo_idx="5" x="33" y="34" z="20" phi="-116" theta="79" psi="-140" CCC="0.428498" model="0.000000"/>
+ <object subtomo_idx="5" x="30" y="15" z="5" phi="-6" theta="82" psi="108" CCC="0.498885" model="0.000000"/>
</subtomo>
<subtomo>
- <object subtomo_idx="6" x="17" y="35" z="7" phi="48" theta="83" psi="122" CCC="0.416486" model="0.000000"/>
+ <object subtomo_idx="6" x="18" y="20" z="24" phi="160" theta="81" psi="-103" CCC="0.475971" model="0.000000"/>
</subtomo>
<subtomo>
- <object subtomo_idx="7" x="18" y="20" z="23" phi="-171" theta="105" psi="-101" CCC="0.430668" model="0.000000"/>
+ <object subtomo_idx="7" x="16" y="33" z="7" phi="-128" theta="96" psi="116" CCC="0.458083" model="0.000000"/>
</subtomo>
</objlist>
diff --git a/test/s68/tm/config.py b/test/s68/tm/config.py
index 046548b..768b0eb 100644
--- a/test/s68/tm/config.py
+++ b/test/s68/tm/config.py
@@ -22,7 +22,7 @@ tomogram = input_folder + tomoID + ".test1.lps25.mrc"
black_on_white = 1 # The contrast of tomogram, 0 if the particle has white contrast (positive values)
templates = [input_folder + "mono-8Apx-lps30-box30-rot12-core.mrc"]
-contour_level = [0.2]
+contour_level = [0.2]# Level it empty if you can't decide, we could calculate it internally
# Masks are required to be the same shape as the templates
# One can create the mask in Relion with soft edges, extend 2 and soft 3 is recommended
masks = [
--
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