autoPACK: INSTALLATION for Cinema 4D (includes autoPack & ePMV in one package)

This early installation for autoPack is an alpha version- use at your own risk and save frequently.

uPy (ubiquitous Python API) enables ePMV and autoPack to work in Autodesk 3ds Max, Maya, Cinema 4D, SoftImage, Blender and DejaVu by writing only one plugin instead of >5.

ePMV (embedded Python Molecular Viewer) provides all of the capabilities of molecular graphics and molecular mechanics software directly in your C4D GUI.

autoPack positions 3D geometries into, onto, and around volumes with minimal to zero overlap. autoPack mixes several packing approaches and procedural growth algorithms. autoPack can thus place objects with forces and constraints to allow a high degree of control ranging from completely random distributions to highly ordered structures.

cellPack is a specialization of autoPack that generates probabilistic 3D models of large sections of cells that can contain dozens to trillions+ of molecules. It can position these molecules to recapitulate observed data where available and can further optimize the molecular interactions on a local level as each molecule is placed into a mesoscale model.

If you have experience with 3D software, especially with C4D, the manual installation should take less than 3 minutes on a Mac and the one-step installer should take less than 6 minutes.

If you encounter difficulties, please visit the forum to search for answers or ask questions.

Prerequisites

1. Maxon's Cinema 4D (C4D) r12–r22
1. If you have a different version, you can download the latest demo here to try ePMV and autoPack
2. Uninstall any previous version of ePMV (and autoFill and autoPack)
1. Navigate to to your C4D preferences as described in step II in the Installation of the uPy... section below
2. Move the ePMV folder from .../plugins to your trash (or just pull it out into the MAXON folder in case you want to revert to it later)
3. Install X11 for Mac : X11 - XQuartz

Installation (C4D r13–22) of the uPy Plugin Package with ePMV & autoPack

1. Open Cinema 4D
2. Locate your Cinema4D preferences folder
1. To ensure you have the correct preferences folder:
1. In Cinema 4D's menu, go to Edit->Preferences
2. Click [Open Preferences Folder] button
1. You'll see the Preferences window now open in your Finder with a path/name similar to:
1. /Users/Library/Preferences/MAXON/CINEMA 4D R16_AB12BC3E/ (the number at the end will be different and may also say R13 through R19)
3. Install the plugin
1. First make sure you have X11-XQuartz installed (if you have recently updated your OS to Catalina (10.15.x or higher), you may need to reinstall XQuartz to get ePMV to work- see Troubleshooting below):
1. Open Spotlight or a finder window and search for 'quartz'. Make sure XQuartz appears. You don't need to launch XQuartz. It is typically installed in your /Applications/Utilities/XQuartz.app folder.
2. If you don't have XQuartz, or want to update it: (see instructions under Prerequisites above (if autoPACK seems to load, but ePMV fails, missing XQuartz is likely the problem)
2. Download the correct zipped package for your system from one of these links:
1. Cinema 4D r20–22 for Mac 64bits upy-C4Dr20-mac.zip
2. Cinema 4D r17–19 for Mac 64bits upy-C4Dr17–19-mac.zip
   
3. Cinema 4D r16 for Mac 64bits upy-C4Dr16-mac.zip
4. Cinema 4D r13–r15 for Mac uPy-aP-eP_c4dR13-R15_mac_1_0_man.zip
3. Unzip the downloaded folder
4. Drag & drop the contents (two folders called ePMV and upy_autoPack) into the ../plugins/ folder of your Cinema4D preferences folder (get correct folder by following step II above):
4. Restart Cinema 4D
5. Launch ePMV, test it, then launch autoPACK and test it as described below
1. You'll find the ePMV plugin under to top menu items:
1. r21-22: C4Dmenu: Extensions/ePMV
2. r13-20: C4Dmenu: Plugins
3. r12: C4Dmenu: Python/Plugins

Troubleshooting

1. ePMV & autoPACK fail to load when running C4D in Mac OS Catalina (version 10.15.x or newer) for all versions of C4D (tested on r19–22)
1. If alerts popup when you open Cinema 4D after installation that look like:
   both ePMV and autoPACK will not be available in your Plugins or Extensions menu.
2. Confirm this is the problem by opening the Python console and searching for lines that say 'ImportError:cannot import name multiarray'. Other files may be missing as well.
3. Nick Woolridge has provided the following explanation and solution:
1. ... this is the aggressive gatekeeper function objecting to some of ePMV/Autopack’s binaries.
2. If you are comfortable using the terminal, use this command: sudo xattr -dr com.apple.quarantine /path/to/folder
1. Replace the '/path/to/folder” bit with the path to your installation of ePMV (in the C4D prefs folder).
   The easiest way to do this is to copy this (make sure not to copy the paragraph return): sudo xattr -dr com.apple.quarantine And paste it into the terminal window.
   Then drag in the relevant folder from the finder (the easiest would be to drag in the “plugins” folder from the prefs folder; make sure there is a space between “com.apple.quarantine” and the folder path).
   This will append the appropriate path to the command. Hit return, and then enter your password when prompted. This will remove the plain from quarantine. Restart Cinema 4D and you should be able to see autoPACK and possible ePMV in the plugins or extensions menu. If you only see autoPACK, then you likely need to reinstall X11 as described below.
2. autoPACK loads, but ePMV fails to load when running C4D in Mac OS Catalina (version 10.15.x or newer) for all versions of C4D (tested on r19–22)
   like You may need to reinstall X11 for Mac, because the locations of certain libraries have changed.
1. Confirm the problem by opening the Python console and searching for lines that mention '... x11...' and unloaded libraries as in '../plugins/ePMV/mgl64/MGLToolsPckgs/pyglf/_glf.so, 2): Library not loaded: /usr/X11/lib/libGLU.1.dylib', etc.
2. Just download and run the .dmg installer: X11 - XQuartz

OPTIONAL:

Complete basic tutorials for ePMV and autoPack

1. If you are new to ePMV or new to molecular graphics, please complete the Basics Tutorial/Survey hybrid. This will guide you through all of the common functions/buttons of the ePMV GUI and simultaneously introduces you to the science and the data types ePMV can work with.
2. This alpha version of autoPack will improve several times each week and the tutorials will expand
1. For now, follow the first steps and then the basic tutorials then experiment on your own. If you find a bug, check the forum to see if its already been fixed, and if not, let us know.
1. Cinema 4D specific tutorials for autoPACK will be posted by January 9, 2013.
2. Find a long list of Cinema 4D specific tutorials for ePMV at http://epmv.scripps.edu/documentation/tutorials
2. Update your ePMV and autoPack software frequently to get the latest performance, stability and functionality enhancements with just a couple clicks directly from within the GUIs!
3. You should add buttons to your startup palette:
1. C4D menu: Window>Customize>CustomizePalettes:
2. In the Customize Commands window type ePMV or auto in the Filter to find the apps then drag and drop each icon where you'd like it.
3. C4D menu: Window>Customize>SaveAsStartupLayout

Improve your software by volunteering to complete the surveys regularly

1. TheInstallation Survey takes less than 30 seconds and will help us improve/simplify the experience.
2. TheePMV Basics Tutorial Survey will help you become an advanced-beginner level ePMV user and molecular artists in <40 minutes. It will also help us improve software performance.
3. A similarly detailed autoPack Basics Tutorial Survey will post by January 9, 2013.



Depricated: Installation(C4D r12)of the uPy Plugin Package with ePMV & autoPack

1. Open Cinema 4D
2. Locate your Cinema4D preferences folder
1. To ensure you have the correct preferences folder:
1. In Cinema 4D's menu, go to Edit->Preferences
2. Click [Open Preferences Folder] button
2. You'll see the Preferences window now open on your desktop with a name similar to:
1. /Users/Library/Preferences/MAXON/CINEMA 4D R12_AB12BC3E/
3. Right (or control) Click on the revealed folder> Get Info: Select and Copy the path under Where: '/Users/userName/Library/Prefere...' for use below.
4. Follow the onscreen instructions. If you run into problems try the manual installation instead or search the forum.
3. Install the plugin
1. One-step Installer (requires Java and is only valid for C4D R12-R15. For R16 and R17, use manual install Option 1 above)
1. One-step installer: uPy-aP-eP_c4dR12-R15_mac_1_0_inst.jar
1. The installer will ask you for the User preferences folder containing the plugin folder
1. Paste in the path you copied in Step II.
2. The installer loads software from our slow educational server and may take 5 minutes even on the fastest of internet connections.
3. Mac C4D users may prefer the manual installation Option 2 below which downloads in < ~1 minute. Both processes install the same software.
4. Restart Cinema 4D
5. Launch ePMV, test it, then launch autoPACK and test it as described below
1. You'll find the ePMV plugin under:
1. r12: C4Dmenu: Python->Plugins
2. r13-16: C4Dmenu: Plugins