*** LoTToR download and user manu ***
1. Download
LoTToR software download
2. Installation:
Linux command>> unzip LoTToR-ver01.zip
3. Related software requirement:
• Linux system
• UCSF Chimera or other software to display 3D map
• Python
4. Input data reqyuirement
• 3D density map/volume
• Tilt angle range and steps
• Molecular mass
• Image apix (A/pixel)
• Mask file
4. Run the MW job
# "usage: ./runMissingWedge.py [input_3Dmap_mrc_no_ext] [3Dmask_mrc_no_ext] [negative_angle] [positive_angle] [iteration_number] [lowpass_var]
# where:
# [input_3Dmap_mrc]: the input MRC 3D density map file to do Missing Wedge correction.
# [3Dmask_mrc]: the input MRC 3D mask density map, cutoff mask is better.
# [negative_angle]: the bottom negative angle for 2D stack.
# [positive_angle]: the top positive angle for 2D stack.
# [iteration_number]: the number of iterations.
# [lowpass_var]: {0/num}, if [lowpass_var]=0, do not add lp; if [lowpass_var]={num}, add cut off lp as {num} pixels.
For example: runMissingWedge_v1p3final.py vol_BP_01 3DMask006-adv -70 70 500 4
5. Reference:
LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure, Xiaobo Zhai, Dongsheng Lei, Meng Zhang, Jianfang Liu, Hao Wu, Yadong Yu, Lei Zhang, Gang Ren, Scientific Reports, (2020), 10, 10489. Doi: 10.1038/s41598-020-66793-1
6. Question? please contact us
Gang (Gary) Ren
Lawrence Berkeley National Laboratory
Molecular Foundry, Room: 2220
1 Cyclotron Road, MS 67R2206
Berkeley CA 94720-8197
Phone: (510) 495-2375; Fax: (510) 486-7268
Email: gren@lbl.gov;
https://rengroup.lbl.gov/