A new software project I work on with Ludovic Autin in Art Olson's lab, can make it a lot easier to make a movie like this, and we distribute it for free. Check out: http://epmv.scripps.edu if you want to try it out. -Graham
en español: http://www.youtube.com/watch?v=PjdPTY1wHdQGPCR active site variations made with Ray Stevens labGraham Johnson2016-06-01 | Composite movie 1 for Ray Let me know when we can release this to the public.4mqsTo3uon LigandBinding 1Graham Johnson2015-05-22 | Here, we use UCSF Chimera to morph between two conformations of the Muscarinic Acetylcholine Receptor M2, program a random walk from one conformation to the next with a preference towards the inactive conformation when the ligand is unbound and towards the active conformation when the ligand binds. We add random walks to the atoms to simulate some intramolecular atomic Brownian motion.ePMV Advanced Molecular Techniques: Step 1Graham Johnson2015-05-22 | Ligand Binding with Atomistic Conformational Changes and Dynamics Step 1. Only 4 keyframes to time roughly when the ligand binds. The motions, binding, color changes etc. are all dynamics tag, modifiers, or small amounts of scripting with Xpresso and Python. Step 2 will replace these rough protein placeholders with dynamic models.UCSF Chimera to view cellPACK model of HIV (Human Immunodeficiency Virus)Graham Johnson2014-12-31 | Here is a very quick screen grab demonstration of how you can use the newest version of the molecular viewer software UCSF Chimera to view cellPACK models. We have HIV_0.1.6 available now (still being polished for Chimera) and other models coming online throughout the next two weeks. Please check back frequently. For more information, and a written version of this tutorial, please visit http://www.cellpack.org/learnKilobots Kilotaxis RaceGraham Johnson2014-09-24 | In Mid August, the Harvard Self-organizing Systems Research group came to UCSF to teach a kilobot programming workshop. In the weeklong class, our group programmed a small swarm of kilobits to walk up a light gradient using a chlamydomonas phototaxis algorithm and an E. coli chemotaxis algorithm.HIV cellPACK HIV-1 version 0.1.6Graham Johnson2014-02-06 | This version of HIV has a 145nm diameter spherical envelope with 12 ENV (envelope glycoproteins) projecting from the surface, 834 MA (Matrix proteins) visible under the surface, 4 VPU and 20 NEF proteins. The bilayer is a normal-mapped texture created from PDB files provided by Jacob Durrant of the LipidWrapper project http://nbcr.ucsd.edu/data/sw/hosted/lipidwrapper This rendering shows neither the human surface proteins nor any of the matrix (interior proteins between the surface and the capsid)Rope in a basket: Aneurysm coil riff off of C4D file started by Nick WoolridgeGraham Johnson2013-12-11 | On the medart list serve a question went around about stuffing a springing rope into a container. Nick Woolridge came up with a file that used tracer objects to create a spline. This is a simpler interpretation of that technique into a soft body to drop a spline into a basket. I'm incredibly impressed that the Bullet Physics Engine (which underlies Cinema 4D's physics) was able to handle this scene so robustly... there are small leaks through the edges that could be fixed with a higher frame interpolation or a thicker basket, but all in all its very stable and fast. I can play this entire scene on my old macbook air (2011) at about 30% of the actual framerate.Sketch N Toon Atoms of small molecule animated sketchGraham Johnson2013-09-01 | Anyone know how to draw one line at a time? Problem is that there are multiple line fragments created by Sketch n Toon's [√]Stroke channel. Then I can "paint in the Ambient occlusion with After Effects as if its being drawn in.3pbt.pdb1_2.movGraham Johnson2013-08-30 | ...sigVizStyleSheet1 1Graham Johnson2013-07-09 | sigViz style options 1 to show activation, deactivation and information flow in the cytoscape diagramMsbA Transporter described via a 3D printed modelGraham Johnson2013-06-20 | ABC molecular transporter described by Andrew Ward PhD with 3D printed model created by Graham Johnson in Art Olson's Molecular Graphics lab at The Scripps Research Institute in 2009.autoPACK HIV1.0 rotation with UCSF Chimeras animation toolGraham Johnson2013-03-27 | Testing Chimera's animation tool in conjunction with autoPACK. Very easy and fast and I highly recommend it for simple animation. This 1.8 implementation has a few minor glitches at least with models this size. I think they plan to fix these very soon. There are some dark frames flashing in now and then when played in quicktime (youtube seems to fix that), the transparency is not animatable. The on major issue is the speed and inability to render comfortably as a background task- not sure why you can drag much larger models around in realtime, but rendering to a movie takes 1-2 seconds per frame at the same resolution and seems to take over your entire computer... probably something to do with getting images off of the graphics card and into memory, but I think the developers have a few fixes in mind for this as well.
Make your own by checking out the tutorials I've posted on the subject: http://www.autopack.org/documentation/tutorials/molecular-viewersautoPACK Lipid test strips for HIV... hack some temporary lipids into your sceneGraham Johnson2013-03-17 | We are refining the lipid packing algorithm and have some issues with the Bullet collision engine not releasing memory, so I can only provide a few patches at a time for now. While we continue working on this, I'll try to make some relevant patches that you may want to zoom in on for your story, and perhaps some "low resolution" patches that you can use for more distant views. Soon we will release the updates that will let you pack your own lipids, so keep updating and stay tuned.UCSF Chimera autoPACK result file (.apr) reader: How to load, beautify, and animate HIVGraham Johnson2013-03-15 | This is a 9 minute instructional video to show you how to load the pre-isovalue'd meshes for any of the HIV cellPACK models available. This early alpha version of Chimera's autoPACK reader has limited functionality, but is quite graceful and easy to use. Here I show you how to: •construct the model into your scene with a quick drag-n-drop •change materials (colors, specularity, transparencies) •setup lights and effects •keyframe animations using the animation GUI •render a final movie.
Remember, you need Chimera 1.8 or newer as shown around 0:18 in this video:http://www.youtube.com/watch?v=Xb5LllzmTws&feature=share&list=UUz7CvhTKmz6wklnQUWcIK8g and as described in this video: http://www.youtube.com/watch?v=SeYIMDIslxI&feature=share&list=UUz7CvhTKmz6wklnQUWcIK8gChimera 1.8 with autoPACK .apr reader to visualize HIV models in realtimeGraham Johnson2013-03-15 | Quick and simple movie made with Chimera 1.8UCSF Chimera 1.8 with autoPACK result file (.apr) reader to view cellPACK models like HIVGraham Johnson2013-03-15 | Here is a quick video to show you how to install the correct version of Chimera that will let you view autoPACK models by simply opening .apr files. The next two videos will show you how to open the models, explore them in the viewport, change representations, and how to set up animations and decent lighting.Chimera: How to open an autoPACK result file in Chimera1.8Graham Johnson2013-01-25 | To load an autoPACK model into Chimera 1.8, you need a nightly build of Chimera that is more recent than January 16. The .apr (autoPACK result) file format should show as an option. I'll provide more comprehensive tutorials once we prepare the correct files, but in the current version, you simply download all of the PDB and/or STL files for a cellPACK recipe of interest into a local folder on your drive, add the .apr files you want to visualize, and open that file. You can then use the tools built into chimera to turn representations on and off, modify representations, and perform analysis like distance and volume calculations. This is an alpha version of this reader build by Tom Goddard of UCSF Chimera- its fast and robust, but I need to fix some compatibility issues with the input files to get the correct orientations. I hope to have the correct files ready by January 26.autoPACK model of HIV 1.4 running in PMV with Screen Space Ambient Occlusion NarratedGraham Johnson2013-01-25 | Ludovic got Screen Space Ambient Occlusion (SSAO) running in Python Molecular Viewer (PMV) about a year ago. More recently, he reconnected our uPy GUI for autoPACK to PMV so we can now load cellPACK results into the amazing realtime system. Such a menacing virus, yet so beautiful to look at with this viewer. Pardon the red/blue background- temporary for testing.
Use this and other software to access the autoPACK plugins and enter a contest to win prizes and cash at http://www.autopack.org/cellpackchallenge2012autoPACK model of HIV 1.4 running in PMV with Screen Space Ambient Occlusion and a Clipping PlaneGraham Johnson2013-01-25 | Ludovic got Screen Space Ambient Occlusion (SSAO) running in Python Molecular Viewer (PMV) about a year ago. More recently, he reconnected our uPy GUI for autoPACK to PMV so we can now load cellPACK results into the amazing realtime system. Such a menacing virus, yet so beautiful to look at with this viewer. Pardon the red/blue background- temporary for testing.
Use this and other software to access the autoPACK plugins and enter a contest to win prizes and cash at http://www.autopack.org/cellpackchallenge2012autoPACK Chimera Viewer HIV 1 0 1Graham Johnson2013-01-25 | Tom Goddard build an autoPACK Result (.apr) file reader into Chimera. I will soon provide tutorials to show you how to download and use this to interface with our autoPACK models, but in the meantime here is a quick demo of the HIV 1.0 model running on my laptop. For more information and to join a contest where you can win prizes and cash for animating these models of HIV, please visit http://www.autopack.org/cellpackchallenge2012 The interface is a bit laggy because Apple Quicktime's screen capture function is still absolutely awful.How to model a small molecule, like Acetylcholine using ePMVGraham Johnson2013-01-11 | You can easily load a protein containing Acetylcholine after finding the 4 digit coordinate and then use ePMV to isolate the ligand as shown in the tutorials, but its much simpler to just download a pdb file of the ligand only to import into a clean C4D-ePMV session as shown. Just takes a couple minutes and provides a properly formatted, minimized version of the small molecule with Hydrogens which you would not likely get if you tried to pull the ligand out of a larger protein complex. Install ePMV (the embedded Python Molecular Viewer) and follow basic or advanced tutorials for Cinema 4D, Blender, Maya, 3D Studio Max at http://epmv.scripps.eduSimple Hierarchical Instancing / Reference System Needed For 3D Studio Max And MayaGraham Johnson2012-11-30 | Please let us know how to duplicate this simple LIVE instancing system in 3D Studio Max 2013 and/or Maya. We need it to teach users how to replicate model customization for an upcoming Scientific Visualization Contest, similar to the Cinema 4D approaches used in these videos: http://www.autopack.org/documentation/tutorials/customize-cellpack-models
Post your approaches on the forum at http://www.autopack.org/support/forum Thank you!3D Studio Max uPy plugins autoPack and ePMV: set up icons/viewport and testGraham Johnson2012-11-22 | How to install the uPy plugins for autoPack and ePMV for 3D studio Max in three easy steps.
I'm breaking down the 3D Studio Max Installation Instructions into three short videos. You have already completed steps 1 and 2: 1) Installed the SciViz plugin from Autodesk (a "one-click" .msi) 2) Run the autoPack 1.0.2 installer
In this video, we will complete the thirds and final step: 3) Set up icons and prepare the viewport to access ePMV
Detailed instructions should be followed at http://www.autopack.org/download/3d-studio-max-installation3D Studio Max uPy plugins autoPack and ePMV: run the uPy one-step installerGraham Johnson2012-11-22 | How to install the uPy plugins for autoPack and ePMV for 3D studio Max in three easy steps.
I'm breaking down the 3D Studio Max Installation Instructions into three short videos. You have already completed step 1: 1) Installed the SciViz plugin from Autodesk (a "one-click" .msi)
In this video, we will complete the second step from start to finish in under 3 minutes: 2) Run the autoPack 1.0.2 installer
In the next/last video we will: 3) Set up icons and prepare the viewport to access ePMV
Detailed instructions should be followed at http://www.autopack.org/download/3d-studio-max-installation3D Studio Max uPy plugins autoPack and ePMV: Install Sci-Viz from AutodeskGraham Johnson2012-11-22 | How to install the uPy plugins for autoPack and ePMV for 3D studio Max in two easy steps.
I'm breaking down the 3D Studio Max Installation Instructions into two short videos. In this video, we will complete the first step from start to finish in under 3 minutes: 1) Install the SciViz plugin from Autodesk (a "one-click" .msi)
In the next video we will: 2) Run the autoPack 1.0.2 installer
Detailed instructions should be followed at http://www.autopack.org/download/3d-studio-max-installationePMV: Make an efficient Clathrin Cage in 3d Studio Max using Biological Unit feature of ePMVGraham Johnson2012-11-18 | ePMV (embedded Python Molecular Viewer) is a molecular graphics engine we've developed for 3 years that is now available for 3d Studio Max 2013-64.
This is an informal/unscripted tutorial showing you how to make an efficient "Clathrin" cage using the instancing approach built into the "Biological Unit" function of ePMV. It shows speed enhancements and how to overcome a minor bug to update the changes you make to your coarseMolecularSurface in ePMV version 102.
Please visit http://www.autopack.org/download/3d-studio-max-installation to install this free plugin and update it from within the GUI frequently to get all of the latest functionality and performance enhancementsClathrin 3ds Biounit2Graham Johnson2012-11-16 | ePMV (embedded Python Molecular Viewer) is a molecular graphics engine we've developed for 3 years that is now available for 3d Studio Max 2013-64.
This is an informal/unscripted tutorial showing you how to make an efficient "Clathrin" cage using the instancing approach built into the "Biological Unit" function of ePMV.
Please visit http://www.autopack.org/download/3d-studio-max-installation to install this free plugin and update it from within the GUI frequently to get all of the latest functionality and performance enhancementsOverview of ePMV and molecular graphics for 3d Studio Max 2013 ePMV Alpha2Graham Johnson2012-11-16 | ePMV (embedded Python Molecular Viewer) is a molecular graphics engine we've developed for 3 years that is now available for 3d Studio Max 2013-64.
This is an informal/unscripted overview of the basic principles of molecular graphics and the functions of the buttons available in the alpha2 release of ePMV.
Please visit http://www.autopack.org/download/3d-studio-max-installation to install this free plugin and update it from within the GUI frequently to get all of the latest functionality and performance enhancementsautoPack HIV Viz Challenge Customize Spike Proteins in Maya / 3ds w/ WalkCycle Robot Spike Render?Graham Johnson2012-11-14 | autoPack pre-alpha testers. Please let me know if you are currently able to duplicate this procedure in Maya or 3D Studio Max. We want users to be able to customize the models as efficiently as possible for the uFpcoming cellPack HIV Visualization Challenge: http://www.autopack.org/cellpackchallenge2012
The process is quite simple in C4D- if you can duplicate it in Maya or Max, please post or send a screengrab or written instructions. Thanks, G http://www.autopack.org/cellpackchallenge2012autoPack HIV Viz Challenge Customize Spike Proteins in Maya / 3ds Max with WalkCycle Robot Spike?Graham Johnson2012-11-14 | autoPack pre-alpha testers. Please let me know if you are currently able to duplicate this procedure in Maya or 3D Studio Max. We want users to be able to customize the models as efficiently as possible for the uFpcoming cellPack HIV Visualization Challenge: http://www.autopack.org/cellpackchallenge2012
The process is quite simple in C4D- if you can duplicate it in Maya or Max, please post or send a screengrab or written instructions. Thanks, G http://www.autopack.org/cellpackchallenge2012autoPack HIV Visualization Challenge Customize Spike Proteins in Maya or 3d Studio Max?Graham Johnson2012-11-14 | autoPack pre-alpha testers. Please let me know if you are currently able to duplicate this procedure in Maya or 3D Studio Max. We want users to be able to customize the models as efficiently as possible for the uFpcoming cellPack HIV Visualization Challenge: http://www.autopack.org/cellpackchallenge2012
The process is quite simple in C4D- if you can duplicate it in Maya or Max, please post or send a screengrab or written instructions. Thanks, G http://www.autopack.org/cellpackchallenge2012autoPack and ePMV Installation tutorial for 3ds max 2013: install uPy plugins ePMV & autoPackGraham Johnson2012-11-14 | This video is out of date. Please find the new instructions for 3D Studio Max or any other host at: http://www.autopack.org/install
This video series will walk you through the necessary steps to prepare 3ds Max 2013-64 to run autoPack and ePMV! As described in the detailed written instructions at http://www.autopack.org/download/3d-studio-max-installation, you will install:
1) unzip the uPy plugin ofder
2) unblock two files
3) Install the files and folders as instructed
These videos will walk you through the entire process and the next video will show you how to install and run the plugin. After that you can follow our basic use tutorials which will rapidly expand in the coming weeks. Thank you, GrahamautoPack and ePMV Installation tutorial for 3ds max 2013: access and test ePMV and autoPack in 3dsGraham Johnson2012-11-09 | This video series will walk you through the necessary steps to prepare 3ds Max 2013-64 to run autoPack and ePMV! As described in the detailed written instructions at http://www.autopack.org/download/3d-studio-max-installation, you will install:
1) Customize the 3ds GUI to access you new uPy plugins ePMV and autoPack
These videos will walk you through the entire process and the next video will show you how to install and run the plugin. After that you can follow our basic use tutorials which will rapidly expand in the coming weeks. Thank you, GrahamautoPack and ePMV Installation tutorial for 3ds max 2013: PreRequisite Installations!!!Graham Johnson2012-11-09 | This video will walk you through the necessary steps to prepare 3ds Max 2013-64 to run autoPack and ePMV! As described in the detailed written instructions at http://www.autopack.org/download/3d-studio-max-installation , you will install:
3) Set paths for Python to be accessed by your system
These videos will walk you through the entire process and the next video will show you how to install and run the plugin. After that you can follow our basic use tutorials which will rapidly expand in the coming weeks. Thank you, GrahamautoPack and ePMV Installation tutorial for 3ds max 2013: UninstallingGraham Johnson2012-11-09 | If you are a preAlpha Tester you need to follow these instructions to uninstall the previous versions and then follow the new installation instructions with all of the new file links. These videos will walk you through the entire process. Thank you, GrahamautoPack alphas versions available for 3ds Max 2013 64bit HIV VIEWER tutorialGraham Johnson2012-11-09 | Thanks to Ludovic Autin (uPy) and Christopher Diggins (Autodesk) with support from Chris Andrews (Autodesk):
We now have skeleton alpha versions of autoPack and ePMV available to users of Autodesk 3D Studio Max 2013-64!
Here is an unscripted tutorial to show you how to use the most basic features of the filler tab for two test Recipes that come with autoPack.
Visit http://autopack.org to download this free software and get started today.autoPack alphas versions available for 3ds Max 2013 64bit 2D packing test files tutorialGraham Johnson2012-11-09 | Thanks to Ludovic Autin (uPy) and Christopher Diggins (Autodesk) with support from Chris Andrews (Autodesk):
We now have skeleton alpha versions of autoPack and ePMV available to users of Autodesk 3D Studio Max 2013-64!
Here is an unscripted tutorial to show you how to use the most basic features of the filler tab for two test Recipes that come with autoPack.
Visit http://autopack.org to download this free software and get started today.ePMV alphas versions available for 3ds Max 2013 64 bit Polio Virus tutorialGraham Johnson2012-11-09 | Thanks to Ludovic Autin (uPy) and Christopher Diggins (Autodesk) with support from Chris Andrews (Autodesk):
We now have skeleton alpha versions of autoPack and ePMV available to users of Autodesk 3D Studio Max 2013-64!
We now have skeleton alpha versions of autoPack and ePMV available to users of Autodesk 3D Studio Max 2013-64! Sorry for sluggish frame rate- I'm working in windows on a virtual machine on the Amazon Cloud from my mac to test the software.
get started at http://autopack.org2DcylinderFill3Graham Johnson2012-11-05 | ...autoPack Cylinder test fileGraham Johnson2012-11-05 | This is a rendering of the 2D Cylinder & Spheres Test file that comes with our autoPack software. I clicked into the Recipe Options Tab to alter the default settings: I increased the density of the Cylinders attempted to pack, and freed them to allow for full 3D restrictions instead of restricting the cylinders to rotate only on the packing plane. This also uses the Panda Bullet Engine for fully collision detection/avoidance during packing. Pretty fun effect for something straight out of the open source box.ePMV MayaViewport2Graham Johnson2012-09-27 | Testing Maya's Viewport 2.0 with ePMV. SnapZpro no longer works with OS10.8 (mountain lion) on a mac, so I have to use the builtin quicktime screen capture which made everything painfully slow, but check it out on your own! I hope Cinema 4D builds this functionality someday soon... its been 3 years!autoFill rigid body placement of spheres in realtimeGraham Johnson2012-08-28 | Ludovic got a nice uPy version of autoFill working and we've started to patch together a pretty clean and useable v0.1 GUI. Watch closely to see the autoFill packing algorithm use one of its local packing options (rigid-body relaxation) to avoid collisions. When a point gets selected to place a sphere, all of the previously packed neighbors are used for collision relaxation, the relaxation usually occurs to fast to see it, but you'll see some spheres near the center of each cluster move a bit if they were overlapping at the start. This is a fast choice for packing if you don't update the viewport every step of the way! Will post other local packing options soon.Cinema 4D r14 bug- menus disappear upon foldingGraham Johnson2012-08-09 | Our plugin, ePMV has a nice stable GUI in C4D r12, but in r13 and now in r14, the menus sections disappear when folded shut. We hope this can be resolved with the full release of r14 next month (update March 2014- still persists in R15). r14 is an amazing upgrade otherwise!Cinema 4D r14 openGL bugGraham Johnson2012-08-09 | Running the August 8th demo version of Cinema 4D on my macbook air (1.8GHz i7, 4GBram, OS10.7.4), you see that I need to turn off OpenGL in the preferences to get acceptable performance for the simplest of tasks... takes several seconds to build a cube and it goes to shortcut redraws if you try to interact. I'm sure this will be fixed soon by Maxon and I applaud them for releasing immediately after announcing r14 rather than making us wait a month as in past years! See more extensive discussion and temporary hack solutions at http://www.c4dcafe.com/ipb/topic/70230-cinema-4d-r14-demo-version-available-immediately/page__st__40autoCell View And Build testsGraham Johnson2012-07-20 | autoFill builder file generates a 2D sphere fill test in 1.2 seconds. HIV viewer file loads data from a previous fill stored in our online databases into a uPy host. checkout upy.scripps.edu and autofill.scripps.edu for details