Megan Riel-Mehan featured in USCF Science in Focus article

posted Nov 22, 2016, 11:56 AM by Graham Johnson   [ updated Nov 22, 2016, 11:56 AM ]

Megan's work with Lillian Fritz-Laylin, Dyche Mullins, and Tom Goddard is briefly described in a UCSF Science in Focus article

In a quote from the article, Megan says:
“This project exemplifies the wonderful interplay that can exist between experimental science and visualization science. It makes the case that visualization should be part of the research process, not just something you do at the very end for an article cover.”

YouTube Video

HHMI illustration brought back to life

posted Oct 27, 2015, 6:36 PM by Graham Johnson

Some of Johnson's old DNA repair images have been brought back by HHMI to illustrate HHMI Investigator Paul Modrich's 2015 Nobel Prize in Chemistry:

Best Blender Animation Ever (uses ePMV too!)

posted Feb 23, 2015, 7:06 PM by Graham Johnson   [ updated Feb 23, 2015, 7:22 PM ]

Chris Hammang, a Biomedical Animator at Garvan Institute of Medical Research and CSIRO has created many stunning animations while simultaneously taming the savage beast I know as the open-source 3D animation software package Blender.  Please check out this captivating animation (gorgeous, regardless of the software used, but arguably the best Blender animation I've ever seen) that uses ePMV to generate molecular representations, and check out his other movies from his website.

Immune Defense kickstarter 16 days

posted Jan 9, 2015, 1:02 PM by Graham Johnson   [ updated Jan 15, 2015, 8:10 PM ]

I've worked on many prototypes and have provided consultation on many iterations of Immune Attack and Immune Defense over the years.  The project inventor and leader Melanie Stegman is extremely enthusiastic about teaching complex topics like immunology in a more intuitive manner to a variety of audiences through gaming.  She now has several years of game design and development experience under her belt, but such projects are difficult to fund through traditional government grants.  If you believe that games can aid in student centered learning, please checkout her Kickstarter funding page.

Melanie writes:
We are trying to teach molecular cell biology, and immunology is the story we use to tell it.  We are trying to present the function and some of the context for the happenings at the meso level... our proteins "projections" that are 100x bigger than actual proteins... but we can use Immune Attack to begin to talk about scale, about diffusion, random events, and even fractional occupancy, concentration dependent events, localization of proteins, and specificity of interactions... in addition to molecular mechanisms of host-pathogen interactions.

Happy Holidays

posted Dec 17, 2014, 3:16 PM by Graham Johnson

Have a joyous winter break and enjoy this card that Mesoscope student intern Thao P. Do created in collaboration with Graham Johnson for the UCSF Chimera 2014 Holiday card as described by Tom Goddard and Elaine Meng from RBVI below. Click the USE tab to see how Chimera can be used to view and analyze cellPACK models. Please feel free to print the card for your emergency Holiday needs.

A cellPACK model of bacterium Mycoplasma mycoides 
Behold a computer-generated model of the tiny bacterium Mycoplasma mycoides. The long orange strand is its circular DNA genome, a million basepairs encoding about 1000 genes. This bacterium lacks a cell wall but is covered with lipoglycans, shown here as green filaments. In red, yellow, blue, and purple are various proteins, represented by the structures of homologous proteins from other organisms. Together, these depict the molecular crowding in cells. This model was made with the cellPACK* software ( described in cellPACK: A virtual mesoscope to model and visualize structural systems biology, Johnson et al., Nat Methods (2014). cellPACK models can be viewed interactively with the program UCSF Chimera ( from the Resource for Biocomputing, Visualization, and Informatics**

Funding: * NSF Predoctoral Fellowship (07576), NIH P41GM103426 & P50GM103368, Autodesk, & Mary Anne Koda-Kimble Seed Award for Innovation. ** NIH/NIGMS Biomedical Technology Research Center (P41GM103311). 

M. mycoides in Snow by RBVI associates Graham T. Johnson & Thao P. Do of and, ©2014

Behold HIV-1_0.1.6

posted Sep 24, 2014, 8:47 PM by Graham Johnson

We finished the cellPACK model of the latest detailed version of HIV-1_0.1.6 which will be available in the new versions of cellPACK being released in October and later in the online cellPACK database we are prototyping.

Johnson wins 2nd place Biophysical Society Annual Meeting 2014 Image Contest

posted Mar 6, 2014, 3:15 PM by Graham Johnson

Dynein motor proteins moving along microtubules– 
This ePMV model of Dynein by Graham Johnson is rendered in Cinema 4D and based on a crystal structure reported by Carter, Cho, Jin and Vale (Science- March 4, 2011).

Ritisha Laungani receives Allan Kuchinsky Student Award

posted Oct 23, 2013, 4:27 PM by Graham Johnson   [ updated Oct 23, 2013, 4:28 PM ]

sigViz Google Summer of Code (GSoC) Student Ritisha Laungani received the Allan Kuchinsky Student Award today for her work on fluxViz over the summer of 2013.
 Allan Kuchinsky                     Ritisha Laungani

VIVID Sydney presentation posted

posted Oct 7, 2013, 12:01 PM by Graham Johnson

Here is a talk I gave to describe the work that I and other medical/molecular illustrators do to a general audience attending Sydney's winter light and music festival VIVID.

Lecture at Faraday Discussion 169 in May, 2014

posted Jul 11, 2013, 1:04 AM by Graham Johnson

Graham will speak at the Faraday Discussion in 2014
visit for details.

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