UCSF Chimera autoPACK Installation

These instructions are out of date as of December 2014.

Please use the newest instructions for loading cellPACK models, including HIV, via UCSF Chimera as described here on the new cellPACK website: http://www.cellpack.org/use

There is also a new video describing the new, much simpler procedure on that page.

Thank yo

Deprecated instructions below:

autoPACK: INSTALLATION for UCSF Chimera (molecular visualization & analysis software package)

Overview

This installation uses a preview, "nightly build" of Chimera that provides an autoPACK result file (.apr) reader

Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics, funded by the National Institutes of Health (NIGMS P41-GM103311).

Pre-requisites

1. Windows, Mac, or Linux

2. Respect the license that you will agree to during installation.

Installation of a version of UCSF Chimera that includes the autoPACK result (.apr) reader

1. Install the nightly build of Chimera 1.8

   1. 1. Select the most recent daily build for your specific system and follow the installation instructions

      2. You can confirm this process or follow along and learn some extra information by watching the installation/overview(light) video at the bottom of this page

Load an autoPACK result (.apr) file into Chimera

1. Download the following zipped files

   1. ChimeraSTLrightOldNames.zip

   2. ChimeraSTLs_HIV_BloodPlasma.zip

   3. ChimeraPDBs_HIV_BloodPlasma.zip

   4. Drag any of the .apr files onto the Chimera application icon or inside Chimera select File>Open and navigate to an .apr file in one of the folders downloaded in step I

      1. The model will open with the Multiscale modeling tool visible

      2. Left click to rotate, middle mouse to pan, right mouse or scroll to zoom

Load additional geometries for HIV into Chimera

1. Download then Drag and drop or Open the corresponding bilayer geometry into your Chimera HIV scene

   1. 1. For HIV_1.0–1.2 download and open HIV_EnvelopeBilayer_Rep_Low_1.00.stl to view a half "shell" that coarsely represents the space occupied by the lipids

      2. For HIV_1.3–1.6 download and open HIV_EnvelopeBilayer_Rep_Low_1.03.stl to view a full "shell" that coarsely represents the space occupied by the lipids

• 1. To load the full-resolution lipid bilayer (expensive/slow, but worth it), download the corresponding .zip folder below and drag the .apr into your chimera session where the same numbered HIV is already opened:

     1. HIV_1.2_Lipids_1.00.zip

     2. HIV_1.3_Lipids_1.00.zip

     3. HIV_1.4_Lipids_1.00.zip

Complete basic tutorials for autoPACK Chimera

• 1. This alpha version of autoPACK will improve several times each week and the tutorials will expand

• • 1. Follow the video tutorials to learn how to select and modify properties like colors and transparency or how to set lights and depth cuing properties for any model type.

    2. Molecules from the .stl folder are "dead" meshes that you can only change basic properties

    3. Molecules from the .pdb folder can change representations and perform analysis like distance measurements using all of the standard tools in chimera

    4. Follow the tutorials for a basic overview and check back frequently for new tutorials

    5. We are making frequent and major additions and adjustments to this software, so please check back here frequently to get the latest performance, stability and functionality enhancements!

Improve Tips and Tricks

• 1. Drag any of the "...apr" files onto Chimera's icon (or choose "open"), and the model should open with the Multiscale modeling tool visible.

  2. You can open multiple .apr files into the same scene, for example, you can load HIV 1.4 and then open the HIV 1.4 envelope.stl file or the HIV 1.4 lipid bilayer to augment/complete the model.

  3. You can use the regular models panel to turn things on and off and the multiscale model to modify representations as per usual (change colors, change representation to ribbon or something.)

  4. Here is the big secret trick. This early alpha version for Chimera looks for PDB files for each ingredient first and uses that. If it doesn't find that, it looks for .stl versions. The .stl will give you the same representations you see in the uPy viewer, but you can really only edit their color and transparency etc.... dead meshes.

  5. If you want to swap in a few key PDBs for now, grab them from this database and just change the name to be the same as the .stl file, but with .pdb tag. You can load any of the appropriate surface representations for each of the models in as well... this is just a bilayer shell as a mesh that you can make transparent.

  6. Tom Goddard is also going to adjust Chimera so it can use BIOMT units to make more efficient multimeric models instead of the full biounit PDBs. He's also working on a hardware instancing system to improve the already amazing performance.