Installation of MrParse

MrParse is distributed with the CCP4 software suite, however to get the most out of MrParse you may wish to install some additional software.

Additional Software

MrParse attempts to classify the sequence according to its secondary structure and whether any regions are expected to be Coiled-coil or Transmembrane.

For the coiled-coil and transmembrane classification we need to install the following software:

  • Deepcoil

  • TMHMM

By default MrParse performs a PDB search using PHMMER (distributed with CCP4). However, if installed you can also use HHSEARCH.

Deepcoil

DeepCoil requires python>=3.6.1 and pip>=19.0 for installation. The most simple way to install Deepcoil is with pip:

pip3 install deepcoil

Full installation instructions can be found on the Deepcoil Github page.

TMHMM

TMHMM supports python>=3.5. The most simple way to install TMHMM is with pip:

pip install tmhmm.py

Full installation instructions can be found on the TMHMM Github page.

Note

The GitHub page says TMHMM is only supported on Linux, but we have also be able to run it on MacOS.

HHSEARCH

HHSEARCH can be installed with HH-suite3. The simplest way to install HH-suite3 is via conda or docker:

# install via conda
conda install -c conda-forge -c bioconda hhsuite

# install via docker
docker pull soedinglab/hh-suite

Full installation instructions can be found on the HH-suite Github page.

Note

You will also need to download a database for HHSEARCH, available here. We recommend installing the latest version of the PDB70.

Note

To use HHSEARCH with MrParse we must update the BioPython installation shipped with CCP4, this can be done with the following command:

ccp4-python -m pip install --upgrade biopython==1.76

Config file

MrParse ships with a configuration file ($CCP4/share/mrparse/data/mrparse.config) that can be modified to ensure all executables and databases are found.

_images/config.png

By default, MrParse expects the TMHMM, Deepcoil and HHSEARCH to be callable from the command line as tmhmm, deepcoil and hhsearch respectively.

If --tmhmm_exe, --deepcoil_exe, --hhsearch_exe and/or --hhsearch_db flags are used, the configuration file will automatically be updated and the flags will not be required for future runs. If you wish to change the default search engine, the configuration file can be directly altered.