Software Installations

This page is to document how to install popular software programs related to sequence and structural analyses. ssbio wraps a lot of these programs with Python functions to execute them (some thanks to Biopython), as well as provides parsers for the output files.

Table of Contents

• Sequence tools

  • EMBOSS programs (needle and others)
  • SCRATCH

• Structure tools

  • MSMS
  • DSSP
  • STRIDE

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Sequence tools

EMBOSS programs (needle and others)

Quick links:

• Home page: http://emboss.sourceforge.net/

Installation for Ubuntu/Linux

1. Install the EMBOSS package which contains many programs

    sudo apt-get install emboss
   

2. And then once that installs, try running the "needle" program:

    needle
   

SCRATCH

Quick links:

• Home page: http://scratch.proteomics.ics.uci.edu/
• Download (for SSpro and ACCpro): http://download.igb.uci.edu/#sspro

Installation for Ubuntu/Linux

wget http://download.igb.uci.edu/SCRATCH-1D_1.1.tar.gz
tar -xvzf SCRATCH-1D_1.1.tar.gz
cd SCRATCH-1D_1.1
perl install.pl

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Structure tools

MSMS

Quick links:

• Download: http://mgltools.scripps.edu/downloads#msms
• Home page: http://mgl.scripps.edu/people/sanner/html/msms_home.html
• Manual: http://mgl.scripps.edu/people/sanner/html/msms_man.html
• Paper: http://mgl.scripps.edu/people/sanner/html/papers/msmsTextAndFigs.pdf

Installation for Ubuntu/Linux

1. Download from here: http://mgltools.scripps.edu/downloads#msms, under the header "MSMS 2.6.X - Current Release"

2. Under "MSMS 2.6.1 - Current Release" download the "Unix/Linux i86_64" version - if this doesn't work though you'll want to try the "Unix/Linux i86" version later.

3. Download it, run:

    sudo mkdir /usr/local/lib/msms
    cd /usr/local/lib/msms
    sudo tar zxvf /path/to/your/downloaded/file/msms_i86Linux2_2.6.1.tar.gz
   

4. Link the programs (or add the location to your PATH)

    sudo ln -s /usr/local/lib/msms/msms.i86Linux2.2.6.1 /usr/local/bin/msms
    sudo ln -s /usr/local/lib/msms/pdb_to_xyzr* /usr/local/bin
   

5. Fix a bug in the pdb_to_xyzr file (see: http://mailman.open-bio.org/pipermail/biopython/2015-November/015787.html)

    sudo gedit /usr/local/lib/msms/pdb_to_xyzr
   

   at line 34, change:

    numfile = "./atmtypenumbers"
   

   to:

    numfile = "/usr/local/lib/msms/atmtypenumbers"
   

6. Do the same for the file:

    /usr/local/lib/msms/pdb_to_xyzrn file
   

7. Now try running "msms", it should say

    MSMS 2.6.1 started on structure
    Copyright M.F. Sanner (1994)
    Compilation flags -O2 -DVERBOSE -DTIMING
    MSMS: No input stream specified
   

STRIDE

Installation for Ubuntu/Linux

1. Download the source here: http://webclu.bio.wzw.tum.de/stride/install.html

2. Build the program from source:

    mkdir stride
    cp stride.tar.gz stride
    cd stride
    tar -zxf stride.tar.gz
    make
    cp stride /usr/local/bin
   

3. Try running:

    stride
   

DSSP

Quick links:

• Home page: http://swift.cmbi.ru.nl/gv/dssp/

Installation for Ubuntu/Linux

1. Install the DSSP package

    sudo apt-get install dssp
   

2. The program installs itself as mkdssp, not dssp, and Biopython looks to execute dssp, so we need to symlink the name dssp to mkdssp

    sudo ln -s /usr/bin/mkdssp /usr/bin/dssp
   

3. Then you should be able to run dssp

freesasa

Quick links:

• Home page: http://freesasa.github.io/
• Github: https://github.com/mittinatten/freesasa

Installation for Ubuntu/Linux

NOTE: these instructions are for Ubuntu 17.04 with an Anaconda3 installation

TODO: investigate proper installation

- see: https://github.com/mittinatten/freesasa/issues/15, https://github.com/mittinatten/freesasa/commit/3cdcebdc8c1b21d17d7b36de36a0ab3a9aee458f
- related: https://github.com/mittinatten/freesasa/issues/18

1. Download the latest tarball (see home page), expand it and run

    ./configure --enable-python-bindings CFLAGS="-fPIC -O2"
    make
   

2. Edit the freesasa-2.0/bindings/Makefile, lines 805, 809, 815 to change

    python setup.py [...]
   

   to

    /path/to/anaconda/python setup.py [...]
   

3. Install with

    sudo make install