Documentation for Laueprocess V 3.9
1.Introduction
Laueprocess is a MATLAB-based program for data processing of Laue diffraction images. It has functions for displaying images, analyzing spot sizes, refining crystal orientations, integrating and scaling spot intensities. It incorporates base libraries from Lauegen (liblaue.a) and CCP4 (libccp4c.a, libccp4f.a, libjwc_c.a, libxdl_view.a, libxdl_viewextra.so, libxdl_view.so, libxdl_viewextra.a, libmmdb2.a).
The primary developments of program focus on the interactive potential afforded by Laueprocess to process Laue data sets. Further developments include more automatic processing procedures to complement the interactive functions. Laueprocess should prove particularly useful when batch processing datasets and reprocessing data with a slightly modified set of parameters.
Laueprocess has the function of processing the Laue diffraction data from experiments in protein Crystallography, small-molecule crystallography, and material sciences. It is developed at Shanghai Synchrotron Radiation Facility (SSRF).
Currently, there are several published papers [1-3], which have cited the download link (https://sourceforge.net/projects/laueprocess/files/) of Laueprocess to process Laue diffraction datasets.
References
1. Cheng Pan; Zhijun Wang; Xingyu Gao Automated Orientation and Diffraction Intensity (AODI) Mapping on a Curved Surface. Crystals 2025, 15(3), 200; https://doi.org/10.3390/cryst15030200
2. Li Yu; Zhijun Wang; Cheng Pan; Weizhe Zhang; Bo Sun; Sisheng Wang; Qisheng Wang; Wen Wen; Xingyu Gao; Jianhua He. Single pulse data collection with an X-ray chopper at in situ room temperature Laue crystallography beamline BL03HB. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 2024, 1069, 169891; DOI: 10.1016/j.nima.2024.169891
3. Zhijun Wang; Sisheng Wang; Zhenhuang Su; Li Yu; Yuzhu Wang; Bo Sun; Wen Wen; Xingyu Gao. BL03HB: a Laue microdiffraction beamline for both protein crystallography and materials science at SSRF. Nuclear Science and Techniques. 2024,35, 119; DOI: 10.1007/s41365-024-01475-5
2.Hardware and operation system environment for the program
CPU: Intel(R) Core(TM) i9, 2.61 GHz
RAM: 16.0 GB
Hard disk: 256 G
Operation system: Linux CentOS 7.9 x86_64
3.Download software for installation
Obtain Laueprocess V3.9 from
https://sourceforge.net/projects/laueprocess/files/
For the Laue protein Crystallography experiment, download the package:
laueprocess_protein_V3_9.tar.gz
laueprocess_material_V3_9.tar.gz
4.Install Laueprocess package for Laue protein Crystallography experiment
4.1.Extract laueprocess_protein_V3_9.tar.gz
File structure as:
--- bin.tar.gz
---data.tar.gz
---include.tar.gz
---install_v3_9
--- laueprocess.tar.gz
--- lib.tar.gz
---libgfortran-4.85-44.el7.x86_64.rpm
---libquadmath-4.8.5-44.el7.x86_64.rpm
---xorg-x11-fonts-75dpi-7.5-9.el7.noarch.rpm
4.2.Enter the directory after file extraction, and install using root account
$: su
$: ./install_v3_9
After the installation, and then close the terminal. On the desktop, there are a directory as laueprocess_protein, a parameter file named as template.ldm, and testing dataset, the files in the directory /data/bl03b1/ are shown as:
4.3. Download matlab Linux runtime package from Mathworks website
https://ww2.mathworks.cn/products/compiler/matlab-runtime.html
Download Linux package version number as: R2017b (9.3)
R2017b (9.3) 64-bit Intel 64-bit
Install the download package to /usr/local/MATLAB using the default setting of Matlab runtime package.
4.4.Run laueprocess
Enter the laueprocess_protein directory on the desktop,
run the laueprocess program using the following command from terminal:
./run_laueprocess.sh /usr/local/MATLAB/MATLAB_Runtime/v93
5.Operation of Laueprocess for protein crystallography
5.1. Check the Laue diffraction example data of Lysozyme
5.1.1. Open images
After open the Laueprocess program, input the example data path (/data/bl03b/lys/lys001_001.lau) to check diffraction images, and then press Open Image button. The red color is the marker for spot position.
5.1.2. Adjust the gray level to show spots
The gray level can be adjusted with the Gray low and Gray high Entry box.
5.1.3. Show spots and find spots in the image
Press Show Spots button, red circle marker is shown.
Press Find Spots button, red cross marker is shown.
5.1.4. Reload parameters for the processed dataset
Press the Reload Parameters button to load three Euler angles in red rectangle frame.
5.1.5. Check the predicted spots
From the listbox, select the item of the Euler angle generated by Reload Parameters button , and then the predict spots are shown in the image. Single spots are shown as Green color, overlap spots are shown as Yellow color.
5.1.6. Shown nodals from the processed dataset
The nodal spots can be shown as red cross in the image with the Show Nodals button.
5.1.7. Batch refinement
After input the first file path name (/data/bl03b1/lys/lys001_001.lau) of example diffraction image, then press Batch Refinement button, and the Batch Refinement GUI will show in the left part of Laueprocess GUI.
5.1.8. Select the directory for batch refinement
Input the directory for batch refinement, for the example dataset, input as /data/bl03b1/lys, and then press Select Directory for batch integration button.
All processed diffraction images in the directory will be shown in the listbox, and the information as cell parameters, Euler angle is shown in the listbox. Select or Unselect the diffraction image can be chosen from the listview.
5.1.9.Start intensity normalization
Intensity normalization can be performed using the Start intensity normalization button, on the other hand, the intensity normalization can be recovered using the Undo intensity normalization button.
Intensity normalization is performed in the input directory (/data/bl03b1/lys), the image with maximum intensity is sorted, and then the intensities of all other images are normalized according the selected image.
5.1.10. Set batch refinement parameters
Batch refinement parameters can be adjusted for the spot size, spot border, and dmin, rmin, rmax, lmin, lmax.
5.1.11.Perform the bath refinement
The batch refinement can be performed with the Start Batch Refinement button, and then all diffraction images are processed with the new parameters for refinement and integration, and new integrated mtz files can be generated.
5.2. Start to process new testing dataset of Lysozyme
5.2.1. Preparation of Ldm file
The ldm file has the following format, create a ldm file with the following contents, and save it on the Desktop of CentOS system.
===============================
CRYSTAL Grid8_x20
TITLE xtal
SYSTEM Tetragonal LATTICE P
SYMM 96
BEAM_AXIS +b* ROTATION_AXIS +a*
IMAGE_TYPE smv
IMAGE_DATA i2
DGEOM flat
AXORD +xd-yd
FIDTYPE no
FIDX1 0.0 FIDY1 0.0 FIDX2 0.0 FIDY2 0.0 FIDX3 0.0 FIDY3 0.0
NXRAST 1679 NYRAST 1475
RASTER_SIZE 172
RMIN 11.00 RMAX 120.00
DISTORTION_TYPE ccd
FTHRESH 125.0 FIDBOX 5.00 STHRESH 50.0
OVERLOAD_PIXEL 65000
NUMPACK 1 NPLATES 1
SPOT_EPSILON 0.25
DSPIN 10.0
SPINDLE 0.000
PACK_ID 1
X_CEN_F 868 Y_CEN_F 732
SPACING 0.220
A 78.560 B 78.560 C 37.56 ALPHA 90.0 BETA 90.0 GAMMA 90.0
LMIN 0.6 LMAX 1.580 DMIN 1.9
PHIX 73.823 PHIY -43.194 PHIZ -13.922
CTOF 260.10
Y_SCALE 1.00000
SPOT_LENGTH 1.0 SPOT_WIDTH 1.0 SPOT_FACTOR 0.1 SPOT_BORDER 2.0
SPOT_DELTA 1.0
X_C 0.8834 Y_C -2.3605 W_C 0.0000
TWIST -27.83 TILT -8.12 ROFF 0.000 TOFF 0.000
RFL 1
INT_FTYPE mtz
PROMIN 600.0
OVLIM 0
===============================
The following parameters should be changed in the ldm file according to different crystals (marked as red in the ldm file), SYSTEM, LATTICE, SYMM, Cell parameters, DMIN, SPOT_LENGTH, SPOT_WIDTH, SPOT_FACTOR, SPOT_BORDER.
5.2.2. Copy template.ldm to the Desktop of CentOS system.
There is already a template.ldm on the desktop after installation, the ldm file is used for the lysozyme diffraction data.
5.2.3. Convert image to lau image
Input testing dataset directory /data/bl03b1/lys1 to Directory Entry Box, and input prefix (for example: lys) to Prefix Entry Box, then press Convert button. Wait for the conversion, about 1-2 seconds for each diffraction image. After the conversion, a string as Finish to generate ldm files is shown in the Message box.
5.2.4.Open the lau image
Input the image path (for example: /data/bl03b1/lys1/lys001_001.lau), and then press Open Image button.
5.2.5.Search and select Nodal points
Press the Search Nodals Button. Zoom the image using the mouse to select the intersecting area. Press Add Nodals button to add nodals to the images with the left click of mouse. Select 5-8 nodal points. Press Save Nodals button.
5.2.6. Index the diffraction images
Press Index button to index the Laue diffraction image.
5.2.7. Sort the results of index.
Press Sort Index button, and wait the program to finish
5.2.8. Select the first item to check the pattern.
5.2.9. Adjust the parameters
Adjust the parameters (beamyoffset, beamxoffsest), and then press Refine button, check the rms value from the output of Automatic Parameter Refinement windows.
Set rmax=200, and press Refine button, to fit all spots in the image.
Adjust lmin to fit the diffraction spots near the beamstop, and then press Refine button.
5.2.10. Integrate spots
Press Unfix Cell Par and Unfix Det Par buttons, and press Refine button again, and then Press Integrate button.
5.2.11. Scale spots
Press Scale button, and the Scale GUI is shown in the Left GUI of Laueprocess, and then input the directory path in the Entry Box, Press Select Directory and Check button, and select or unselect mtz files before scale.
Press Start Scale button to scale the data to a specific wavelength
5.2.12.Run aimless and Phenix to find the structure
Start ccp4i, and run aimless, and output scaled mtz file.
Start Phenix, run simple one-component interface, and the structure can be obtained.
6. Install Laueprocess packages for material science experiment
For the Laue diffraction experiment of material sciences, download the package:
laueprocess_material_V3_9.tar.gz, from https://sourceforge.net/projects/laueprocess/files/
Extract laueprocess_material_V3_9.tar.gz
File structure as:
--- bin.tar.gz
---data.tar.gz
---include.tar.gz
---install_v3_9
--- laueprocess.tar.gz
--- lib.tar.gz
---libgfortran-4.85-44.el7.x86_64.rpm
---libquadmath-4.8.5-44.el7.x86_64.rpm
---xorg-x11-fonts-75dpi-7.5-9.el7.noarch.rpm
6.1.enter the directory after file extraction, and then install using root account
$: su
$: ./install_v3_9
After the installation, and then close the terminal. On the desktop, there is a directory as laueprocess_material , and a parameter file named as template.ldm , and testing dataset in the directory /data/bl03b1/blade and /data/bl03b1/blade1 . The processed dataset is located in /data/bl03b1/blade , and the original dataset is located in /data/bl03b1/blade1 .
6.2.Install Matlab runtime
Download matlab Linux runtime package from Mathworks website, and install to /usr/local/
6.3.Run laueprocess
Enter the laueprocess_material directory on the desktop,
run the laueprocess program using the following command from terminal:
./run_laueprocess.sh /usr/local/MATLAB/MATLAB_Runtime/v93
7.Operation of Laueprocess for material science
7.1.Check the data quality from the processed datasets
7.1.1.Open images
After open the Laueprocess program, input the example data path (/data/bl03b/blade/blade001_001.lau) to check diffraction images, and then press Open Image button
7.1.2. Reload parameters for the processed dataset
Press the Reload Parameters button to load three Euler angles.
7.1.3. Check the predicted spots
Select the item of the Euler angle generated by Reload Parameters button in the listbox, and then the predict spots are shown in the image. Miller indices can be observed by the Find HKL button.
7.2. Automatic processing dataset from material science
7.2.1. Convert image to lau image
Before the conversion, files in /data/bl03b1/blade1 are shown as:
Input testing dataset directory /data/bl03b1/blade1 to Directory Entry Box, and input prefix (for example: blade) to Prefix Entry Box, then press Convert button. Wait for the conversion, about 1-2 seconds for each diffraction image.
After the conversion, a string as Finish to generate ldm files is shown in the Message box.
files in /data/bl03b1/blade1 are shown as:
7.2.2.Search Nodals
Press Search Nodals button, and the nodal spots (green spot) is shown in the image.
Press Save Nodals button.
7.2.3.Index
Press Index button, results are shown in the list box.
Press Sort Index button.
Select the first item from the list box, and the predict spots (yellow) are shown in image.
Press Find HKL button to find the Miller indices of the predicted spots.
7.2.4.Refine
Press Unfix Cell Par button, and Unfix Det Par button, and then Refine button.
7.2.5.Integrate
Press Integrate HKL button, and then spots are integrated with circle integrator and rectangle integrator, the size of circle integrator can be modified by Count Spot Size entry box, and the size of rectangle integrator can be modified by Count Border entry box.
7.2.6.Batch Index
Press Batch Index button, and the orientation and integrated intensity can be automatically obtained for each diffraction image.
7.2.7.Show results
Press Show Map button, results are shown in Figure 1-8, Figure 1, Phix map; Figure 2, Phiy map; Figure 3, Phiz map; Figure 4, Beam center X offset; Figure 5, Beam center Y offset; Figure 6, Intensity map constructed by rectangle integrator; Figure 7, Intensity map constructed by circle integrator; Figure 8, The difference map between rectangle integrator and circle integrator.
8. Tutorial Video for material science
Download LaueprocessInstallationVideoformaterialscience.wmv from https://sourceforge.net/projects/laueprocess/files/.
There is a detailed tutorial for automatic batch processing of thousand diffraction images from material science.
9. The MATLAB GUI codes of Laueprocess
The MATLAB GUI (*.m and *.fig files) codes of Laueprocess is available from https://sourceforge.net/projects/laueprocess/files/ with the packages
laueprocess_material_matlab_src.zip for material science and
laueprocess_matlab_src.zip for protein crystallography
For more information, send email to wangzj@sari.ac.cn
Download Latest Version
laueprocess_protein_V3_9.tar.gz (104.7 MB)
