MAINMASTseg

MAIHNMASTseg is a segmentation program for EM maps with symmetry.

Copyright (C) 2019 Genki Terashi, Daisuke Kihara, and Purdue University.

License: GPL v3 for academic use. (For commercial use, please contact us for different licensing)

Contact: Daisuke Kihara (dkihara@purdue.edu)

Cite : Terashi, G., Kagaya, Y. & Kihara, D. MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. J Chem Inf Model 60, 2634-2643 (2020).

Pre-required software

• UCSF Chimera {EM map preparation & visualization} : https://www.cgl.ucsf.edu/chimera/
• Pymol{for visualiztion} : https://pymol.org/2/
• OpenMP library
• C compiler (gcc or clang in Mac)

Installation for MacOS

1. Install Xcode
2. Install Homebrew

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

3. Install OpenMP

brew install libomp

4. Complile code

git clone https://github.com/kiharalab/MAINMASTseg.git<br>

cd MAINMASTseg
rm MAINMASTseg *.o #remove compiled files
make -f MakefileMacOS #For mac

Installation for Linux

1. Complile code

git clone https://github.com/kiharalab/MAINMASTseg.git

cd MAINMASTseg<br>
rm MAINMASTseg *.o #remove compiled files
make

Tutorial

Example1 contains all input files and result files.
Please check http://kiharalab.org/mainmast_seg/Tutorials.html

Input Data

In Example1, there is a map file (emd-0093.mrc). MAINMASTseg requires (1) Density map (mrc format), and (2) Rotation Matrix file.

(Optional) Remove noise from the EM map by UCSF Chimera

Some EM map contains many noise at the recommended contour level.
Before computing segmentation, noise can be removed hideDust command, in UCSF Chimera.

sop hideDust #0 size 100 metric volume

Then save as "MAP_m4A.mrc".

Rotation Matrix file (PDB format)

Make a rotation matrix file by UCSF Chimera

EMD-0093 has C4 symmetry. The map size is (220x1.34,220x1.34,220x1.34). The center of the map is (147.4,147.4,147.4).
In Chimera,

1. open 6gyn.pdb as #0
2. Type the following command in Chimera command line

sym #0 group c4 center 147.4,147.4,147.4  

3. Save all pdbs as symmetry.pdb
4. Extract the rotation matrix from the saved pdb file as:

grep BIOMT[1-3] symmetry.pdb > MTX.txt 

Make a rotation matrix file by phenix.map_symmetry

When the center of the EM map is unknown. phenix.map_symmetry is able to identify the rotation matrix.

phenix.map_symmetry MAP_m4A.mrc symmetry=C4

Then, convert the output file (symmetry_from_map.ncs_spec) to MTX.txt.

../conv_ncs.pl symmetry_from_map.ncs_spec > MTX.txt

Segmentation

MAINMASTseg generates the segmented MST (-M option) and density maps (-W option).

(1) Generate MSTs only with the recommended contour level 0.7.

../MainmastSeg -i MAP_m4A.mrc -Y MTX.txt -c 8 -t 0.7 -M > test.cif

Visualize MSTs by Pymol:

../bondtreeCIF.pl test.cif > a.txt

Open a.txt by pymol:

pymol -u a.txt

(2) Generate segmented density maps

Once you confirmed the MSTs, MAINMASTseg can generate the segmented density maps with -W option:

../MainmastSeg -i MAP_m4A.mrc -Y MTX.txt -c 8 -t 0.7 -M -W > test2.cif

This command will generate 4 mrc-format files (region0.mrc,region1.mrc,region2.mrc,region3.mrc).

Visualization (bondtreeCIF.pl)

This program makes a Pymol script for visualization of MSTs.

bondtreeCIF.pl [Output of MAINMASTseg (CIF format)] > a.txt

Then, the "a.txt" can be used by pymol as

pymol -u a.txt

Generating Rotation Matrix (conv_ncs.pl)

This program convert symmetry_from_map.ncs_spec (output file of phenix.map_symmetry) to the rotation matrix file.

conv_ncs.pl [symmetry_from_map.ncs_spec] > MTX.txt