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XFEL-Fitting-GMM

Asi H, Dasgupta B, Nagai T, Miyashita O and Tama F (2022) A hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data. Front. Mol. Biosci. 9:913860. doi: 10.3389/fmolb.2022.913860

AUTHORS of the program

  1. Bhaskar Dasgupta [email protected] - inp.yaml, Monte-Carlo sampling

  2. Tetsuro Nagai [email protected] - tools dealing with the XFEL difraction images of GMM

  3. Han Asi [email protected] - pipeline program, modification of inp.yaml, modification of Monte-Carlo sampling

  4. Yuki Mochizuki - initial study on XFEL diffraction pattern calculation from GMM

  5. Osamu Miyashita [email protected]

  6. Florence Tama [email protected]

This XFEL fitting program has been developed at Nagoya University and RIKEN.

RELATED PUBLICATIONS

  • Dasgupta, B., Miyashita, O., Uchihashi, T. & Tama, F. Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images. Front Mol Biosci 8, 704274 (2021).
  • Dasgupta, B., Miyashita, O. & Tama, F. Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images. Biochim Biophys Acta Gen Subj 1864, 129420 (2020).
  • Nagai, T., Mochizuki, Y., Joti, Y., Tama, F. & Miyashita, O. Gaussian mixture model for coarse-grained modeling from XFEL. Optics Express 26, 26734 (2018).

HOW TO INSTALL

In the folder 'project':

conda env create -f environment.yml
bash install.sh

HOW TO RUN

  • Before running the code, user need to make an output directory named 's1'. (refer to 'inp.yaml'>'OUTPUT'>'IMAGEPATH', 'STATPATH', 'GMDATPATH')

  • Beg_AK_3.gmm and End_AK_214.gmm are input gmm files of initial and target conformation. They are created from pdb files using following commands:

  afmEmulator -f emulate_Beg_AK.yaml

(afmEmulator is in /project/bin, emulate_Beg_AK.yaml is located at /pipeline/input_files/AK)

  gmconvert A2G -ipdb End_AK.pdb -ogmm End_AK_214.gmm -ng 214

(gmconvert software: https://pdbj.org/gmfit/doc_gmconvert/README_gmconvert.html)

  • Command to run XFEL GMM fitting:
  python pipeline.py inp.yaml Beg_AK_3.gmm End_AK_214.gmm

  • Initial parameters, such as RESTRAINTS, det_width,det_dist, wave_length, SEED, lowest_k, and circle_width are included in inp.yaml.

  • Output setting is in inp.yaml.

NOTES

Tested with python 2.7, anaconda environment only. May not work correctly with python 3.

LICENSING

The program is licensed under the Apache License, Version 2.0. See LICENSE for the full license text.