We are going to prepare an ingredient representing a bacterial ABC transporter ( PDB entry 1L7V). The second ingredient is a membrane protein that we want to distribute on the surface of the compartment. Step 5 Build the ingredient for the compartment surface, using an aligned PDB from OPM (the Orientations of Proteins in Membranes database) Save your work as "myRecipe_comp1_efg.blend". MyRecipe/myRecipe_Setup/myRecipe_compartments_recipes/compartment1_recipe/compartment1_interior In the scene outliner, under Cluster, rename CenterSpheres to elongationFactorĭrag and drop the object elongationFactor under In SphereTreeMaker, in the "SphereTree Build" section, change the "Number of clusters" to a value of 10. This new panel will help you generate spheres covering the protein. This will create an object called "Cluster" in the Outliner with a child called "CenterSpheres", and open the SphereTreeMaker panel at the bottom of the Misc tab. In the autoPACK Utilities section, click on "Create custom Ingredient". This will create an object called 1efg_cloudds in the scene outliner (child of the object called 1efg) with a vertex for every atom. In ePMV - "Atom/Bond Representations" section, click on PointClouds. Rename CoarseMS_1efg to elongationFactor_mesh (Note: all of these names must be entered precisely, because these are the handles autoPACK uses to identify them) Select the object "CoarseMS_1efg" in the scene outliner (it will be under "1efg"). So we have already learned something by making this simple model. This tells us that for objects of this size or greater (which includes most proteins), there is not enough room to pack at a 1.0 Molar concentration. In the "Total to attempt" column, you will also see that we tried to pack 60 of Ingredient1, but could only fit 39. If you want to pack at 200 nanomolar, but want to make sure there is at least one Ingredient packed, you can set it to ".0002 Molar, +1". If you want to pack 10 Ingredients, you can set it to "0.0 Molar +10". You will see that we packed Ingredient1 at "1.0 Molar, +0". For surface ingredients, it is molecules per square nanometer. "Density" for soluble ingredients is in terms of Molarity. The most important for now are the "Recipe options" of "Density" and "+ this many". It has several parameters that you can change to suit your needs. Take a look at the myRecipe Filler v1.0 panel. You can now navigate around to look at the model from different perspectives. We recommend user to check the blender reference manual and the getting started section. Start autoPACK, go to Help->Check for stable Update. Start ePMV (push the button, ePMV will appear in the Misc Tab on the left), at the top of the ePMV window, click Help->"Check for stable updates". Restart Blender, ePMV and autoPACK should appear on the top right of the window. On the Add-ons tab, check the boxes for "System: autoPack", "System: ePMV", and "System: ePMV synchro" (easiest to find if you first click on the "System" Category on the left) Navigate to upy-addons.zip and install it (double-click or push the "Install from File." button) Install add-ons upy-addons.zip using blender user preferences interface.Ĭlick the "Install from File." button at the bottom Unzip and move the contents of the extracted folder (MGLToolsPckgs and upy-addons.zip) into the Blender folder (where the executable is) Windows 64bits Blender 2.78 (python 3.5) Windows 64bits Blender 2.76 (python 3.4) upy-Blender-win-64.zip Linux 64bits Blender 2.78c (python3.5) upy-Blender-Linux-P圓5.zip Linux 64bits Blender 2.7x (python3.4) upy-Blender-linux-64.zip Mac OS 64bits Blender 2.7x upy-Blender-mac-64.zip uPy Plugin Package with ePMV & autoPackĭownload plugins, depending on which system you're using: If the plugin doesnt start, try to install the visual C++ redistributable for vs2015 We highlight in red in the tutorial when you should expect a crash :( The current version of the plugin seems unstable and tend to crash. Open the blender.app Package Content with Finder, browse to Content/MacOS/ and then run blender) If you have trouble getting the plugin to run, try running blender from the executable directly.
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