Docker saves the day – Roadmaps – rivem – Biochemistry Computational Research Facility (BCRF)

Roadmap details at 5x axis of rhinovirus B14 — Roadmap details at icosahedral 5x axis of rhinovirus B14

Edit: April 8, 2025

Images were updated to remove the error that presented the roadmap in a mirror image.

Docker saves the day!

Here is a great example of how Docker can help save a NATURE paper!

Summary:

Problem: Professor wants to use a specific virology program called rivem (links below.) However, this only works on a Linux system.

Solution: download a small, 64Mb, Ubuntu Docker image and run the rivem program inside a Docker container!

This requires just a few steps:

Step 1: download the program: rivem
Step 2: download relevant 3D PDB data, e.g. rhinoviruses B14, A16, and C15 from the Protein Data Bank
Step 3: download the ubuntu docker image from hub.docker.com with command: docker pull ubuntu
Step 4: start the image with a shared directory containing the PDB data, for example:

docker run -it --rm -v $HOME/dockershare/:/data ubuntu

step 5: go to the appropriate directory and run the rivem command to create the roadmap
Step 6: relish in the result!:

rhino b14 roadmap - small — rhino b14 roadmap – small

Links:

(Formerly available from Purdue as rivem [Archived])
UPDATE: now available from UTEP on programs page downloadable from rivem manual page. Author: Chuan (River) Xiao.

REFERENCES

Xiao C, Rossmann MG, Interpretation of electron density with stereographic roadmap projections. J Struct Biol. 2007 May;158(2):182-7. Epub 2006 Oct 24. PMID:17116403 PMCID:PMC1978246 DOI:10.1016/j.jsb.2006.10.013

Chapman MS, Mapping the surface properties of macromolecules. Protein Sci. 1993 Mar;2(3):459-69.
PMID: 8384042 PMCID:PMC2142375 DOI:10.1002/pro.5560020318

Rossmann MG, Palmenberg AC. Conservation of the putative receptor attachment site in picornaviruses. Virology. 1988 Jun;164(2):373-82.PMID:2835857 DOI:10.1016/0042-6822(88)90550-8