MainMastseg FAQ

Installation

Q. I want to use MAINMASTseg program on MacOSX. But I cannot compile the codes.

A. MAINMASTseg requires libomp and C compiler. To install these libraries, you have to setup Xcode, commandline tools.
  • Install Xcode
    Open App Store. See Xcode
  • Install command line tools
    Open "terminal" from Applications, then
    Type command

    xcode-select --install

  • Install Homebrew
    Type command in terminal window

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

    Confirm the homebrew command

    brew doctor

  • Install OpenMP
    Type command in terminal window

    brew install libomp

  • Complile Codes
    Type command in terminal window

    git clone https://github.com/kiharalab/MAINMASTseg.git
    cd MAINMASTseg
    rm MAINMASTseg *.o #remove compiled files
    make -f MakefileMacOS #For mac

    • Input Data issues

    Q. I do not have the relion program in my PC. How can I greenuce the size of EM map?

    A. If you have a reference pdb file. You can extract the regions within a specific distance of the currently selected atoms (or chains/molecules) by "zone tool" in UCFS Chimera. See Here
  • Example (extract density data around chain A in PDB file)
    1. Select chain A:
      [Chimera menu] select > Chain > A
    2. Segment out around chain A:
      [Volume Viewer Menu] Features>Zone
      Click [Zone] botton.
    3. Save the segmented map:
      [Volume Viewer Menu] File>Save Map as...