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atomdance-docker-chimerax

ver. 1.0-beta

Dockerfile and build for containerized execution of gbabbitt/ATOMDANCE-comparative-protein-dynamics Molecular Dynamics software suite. ATOMDANCE package source is available here:
https://github.com/gbabbitt/ATOMDANCE-comparative-protein-dynamics

How to use this repository

  1. Confirm you have Docker and docker-compose installed.

  2. Determine a path on your host machine that you would like to interact with the docker image for passing analyses to and retrieving data from. This is denoted in Step 4 below as /PATH/TO/SHARED/DIRECTORY and will be mapped in the docker container as /data. This directory must exist and be writable by the image. Sample instructions for enabling this as follows:

mkdir /PATH/TO/SHARED/DIRECTORY && chmod -R 766 /PATH/TO/SHARED/DIRECTORY

  1. Download UCSF ChimeraX and deposit the ucsf-chimerax_1.6.1ubuntu22.04_amd64.deb file in the empty chimerax/ directory included with the repository. This is how atomdance-docker will install UCSF ChimeraX. UCSF-ChimeraX

  2. Set up and run this image locally:

# 1) Clone this repository and its submodules
git clone --recurse-submodules https://github.com/patrynk/atomdance-docker-chimerax.git
# 2) Build the image. This will take a WHILE. 
cd atomdance-docker
sudo su
docker-compose build
# 3) Deploy the image and follow the on-screen GUI. Make sure you are root user each time you execute this (i.e. sudo su)
docker-compose run -u atomuser -v /PATH/TO/SHARED/DIRECTORY:/data atomdance start
  1. To run an analysis, copy your chosen MD files to /PATH/TO/SHARED/DIRECTORY you specified before, and after running the 'docker-compose run' command specified in step 4, substep 3, specify the paths to the files in the ATOMDANCE UI but removing /PATH/TO/SHARED/DIRECTORY. For example, the files
    /PATH/TO/SHARED/DIRECTORY/example.prmtop
    /PATH/TO/SHARED/DIRECTORY/example.pdb
    /PATH/TO/SHARED/DIRECTORY/example.nc

    would become

    example.prmtop
    example.pdb
    example.nc

Known issues:

  • Sometimes CPPTraj hangs with dead processes. Re-starting the analysis will fix this.
  • CHOREOGRAPH 2.0 dependency penguoin does not play nicely with ChimeraX python3.9 installation, working on a venv or other fix for this.
  • ChimeraX visualization functionality not yet working within docker image.

Citations:

Babbitt G.A. et al. 2023. ATOMDANCE: machine learning denoising and resonance analysis for functional and evolutionary comparisons of protein dynamics bioRxiv 2023.04.20.537698; doi: https://doi.org/10.1101/2023.04.20.537698

Babbitt G.A. Coppola E.E. Mortensen J.S. Adams L.E. Liao J. K. 2018. DROIDS 1.2 – a GUI-based pipeline for GPU-accelerated comparative protein dynamics. BIOPHYSICAL JOURNAL 114: 1009-1017. CELL Press.

Babbitt G.A. Fokoue E. Evans J.R. Diller K.I. Adams L.E. 2020. DROIDS 3.0 - Detection of genetic and drug class variant impact on conserved protein binding dynamics. BIOPHYSICAL JOURNAL 118: 541-551 CELL Press.

Babbitt G.A. Fokoue E.P. Srivastava H.R. Callahan B. Rajendran M. 2022. Statistical machine learning for comparative protein dynamics with the DROIDS/maxDemon software pipeline. In press. STAR Protocols CELL Pres

Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.