Ucsf chimera movie tutorial

Tom goddard october 3, 2012 this tutorial shows how to make animations using chimera for use on web sites, in journal articles, and talks. Or you could try a watershed segmentation mouse mode. Examples of commands for making animations with ucsf chimera. Chimera includes complete documentation and is free of charge for academic, government, nonprofit, and personal use. The scripts require a chimera build from march 2012 or later.

The expanded getting started tutorial is more suitable for printing more selfcontained rather than hyperlinked than the above. To start learning how to use chimera, go to help tutorials, or the chimera tutorial. Mar 07, 2012 a tutorial video for creating a morph movie between two conformations of protein structures. Making molecular movies with chimerax executable command links. Ucsf chimera was used to animate the molecules shown in the video. Tom goddard may 5, 2009 ucsf mission bay library goals make simple molecular movies. Ucsf chimera is a free and open source molecular visualizer. Visualizing structures with ucsf chimera for beginners chimera basics. The basic features of chimera are available either way, but not all command functions are available in menus or graphical interfaces, and not all menu or graphical interface functions are available in commands. To follow this tutorial you should be familiar with. Tom goddard, programmeranalyst, ucsf resource for biocomputing, visualization, and informatics hosted by pete meyer recorded on april 11.

In this tutorial, we will learn to superimpose and compare different structures of the same protein. Learn chimera commands that are useful for movie making. This video demonstrates how to create a movie in ucsf chimera for analysis and advanced visualization. Movie making in chimera university of california, san. You can interact with chimera using menus andor commands. Protein visualization with ucsf chimera, video editing with blender, and sound editing with audacity. Dock calculates possible binding modes, given the structures of ligand and receptor molecules. Its possible to update the information on ucsf chimera or report it as discontinued, duplicated or spam. Tom goddard, programmeranalyst, resource for biocomputing, visualization, and informatics, ucsf host. Welcome to this tutorial on superimposing and morphing. You can experiment with the chimera object hierarchy by using the python shell to fetch the file for crambin from the pdb. Open this web page within chimerax using the following chimerax command.

Viewdock tutorial university of california, san francisco. Chimera includes the following approaches for capturing image frames and assembling them into a movie file. There are several different programs and resources that can be used to create videos for this challenge. Ucsf computer graphics lab chimera team and babbitt lab department of pharmaceutical chemistry university of california, san francisco on nov 1, 2010, at 3. Movie recording smooth transition between two scenes. Chimerausers how to mask irregular shape in em density map. Hi chimera users i did simulation of protein by gromacs.

We will use maltotriose binding protein, pdb 2gha, and chimera 1. I notice that some actions in chimera can be undid, such as undo selection or undo move. For example, i colored a selection zone in a different color. Movie recorder is a graphical interface with buttons to start recording, stop recording, and encode the saved images as a movie file. Resubmit failed autodock vina jobs without reconfiguring the gui. Ucsf chimera movie tutorial for the background color change this would have echoed set bgcolor white onto the panel. This allows integration of movie recording and content within a single script. Using chimera, one can generate highquality images and animations. Uses and advantages play video clippings of chimera available on our website. Chimera tutorials a set of tutorials is included in the chimera users guide. To view a web page from within chimerax, start chimerax and use the command open url substituting in the actual url, or navigate here using the chimerax menu.

Tom goddard west coast protein crystallography workshop march 20, 2017 how to make movies showing molecular structures using chimerax. This tutorial provides an overview of basic features in chimera. Chimerax medical imaging in vr features added for niaid. This tutorial shows how to make animations using chimera for use on web sites, in journal articles, and. In this tutorial, we will learn to adjust background lighting and effects. Spin 360 degrees the mother of molecular animations open maltotriose binding protein and make it look good. Chimera movie making university of california, san francisco. Chimera comes preloaded with many helpful tools for analyzing results and making movie files from trajectories. For examples of use, see the trajectory and ensemble analysis tutorial. However, for reproducibility and smoother results, often a chimera command file script will be used instead. If you need to use your window manager to crash chimera in order to escape, dont forget to delete all the temporary files that chimera creates in tmp. A tutorial video for creating a morph movie between two conformations of protein structures. Making movies university of california, san francisco.

How to record molecular animations with ucsf chimera youtube. Chimerax automatically adjusts the appearance and style of the. We will look at galactose binding protein as an example pdb entries 3gbp and 2fw0 run tutorial in chimerax. Hi sy, you could trace curves around your object in a few planes to define a surface and use that surface to mask the map. We will look at galactose binding protein as an example pdb entries 3gbp and 2fw0. Welcome to this tutorial on overview of ucsf chimera. The basics of ucsf chimera this is a very basic introduction to ucsf chimera, a powerful, free software package for visualizing and analyzing macromolecules. In this tutorial we will learn, about ucsf chimera. In short the way it works is you simply add a command like movie crossfade frames 25 to your movie recording chimera command script where you want the transition to occur.

Download and installation of chimera on ubuntu linux operating system. Video tutorials and tutorials from past chimera workshops are also available. Will show how to create 4 simple movies within chimera. Publication images and movies course july 29, 2008 ucsf mission bay library movie overview chimera has only simple movie making capabilities. It can also crash the x window system at this stage. Conformational change tutorial ucsf chimera trajen head. Ucsf 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. This tutorial describes one possible combination ucsf chimera to visualize proteins, and then blender and audacity to edit video together. Ucsf chimera or simply chimera is an 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. You can interact with chimera by using the menus andor by entering commands. Chimera users guide the chimera users guide has three main parts, which are interconnected. Welcome to this tutorial on animation using chimera interface. After creating a movie, it is necessary to restart chimera, because it becomes extremely slow and may crash or hang. Additionally, these two short videos provided by the protein databank will give a brief introduction to the software and walk through several basic, yet important structure analysis tools available within chimera.

Stanford cryoem tutorial looking at bacterial atp synthase. Analyzing molecular assemblies with ucsf chimera presenter. How to aminate conformational change with ucsf chimera. A subtle modification to ucsf chimeras md movie extension to allow the visualization of volumetric data along a molecular trajectory. Highquality images and animations can be generated. Learn the basic functionality of ucsf chimera, such as loading pdb coordinates into the software, manipulating the structure in 3d, and saving your session. Blender tutorial using open babel to generate 3d data to make. With pychimera you can run scripts depending on chimera from cli with pychimera script. Presentation of chimera this introductory course about 3d structure visualization and high quality imaging for publication will make use of the free program chimera. Tutorials exercises ranging from beginnerlevel to more advanced basic func. Ucsf chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. Protein visualization with ucsf chimera, video editing with blender, and sound editing with.

Ucsf chimera was added by stephanf in aug 2016 and the latest update was made in mar 2020. Visualizing structures with ucsf chimera for beginners. This tutorial describes how to visualize and make a movie of a molecular simulation using the freely available program ucsf chimera. How to record molecular animations with ucsf chimera. Movie making tutorial from publication images and movies course july 29, 2008. Ucsf chimera getting started dna helix with bound netropsin this tutorial provides an overview of basic features in chimera for displaying and manipulating structures. Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. Preparing an input design file using cadnano in this tutorial, we will use the. Exercises from july 2008 volume data display course.

The online moviemaking tutorials 2009, 2012 and the chimera animation. Ucsfchimerac4animationenglish script spokentutorial. Movie making in chimera university of california, san francisco. Also, if you are new to video editing, you might want to watch parts 4 and 5 of tutorial 1, where the basic techniques are demonstrated using blender and audacity.

Ucsf chimera is a program for interactive visualization and analysis of molecular structures and related data. Dec 09, 2016 how to record molecular animations with ucsf chimera. Hi camilla, the default movie recording format for the chimera movie command is quicktime. In a dock search, each compound typically from a database of many thousands is treated as a possible ligand, and the structure of a target macromolecule is treated as the receptor. There are several ways to start md movie, a tool in the mdensemble analysis category. Tom goddard, andrew ling updated october 22, 2012 molecular assembly display and analysis. Md movie is a tool for viewing and analysis of trajectories and other ensembles. Jul 12, 2008 after creating a movie, it is necessary to restart chimera, because it becomes extremely slow and may crash or hang. If you are new to the software please watch the tutorial 1, parts 1, 2, and 3 to obtain a basic proficiency. In this tutorial well show how chimera can be used to generate 3d printable molecular models for fdmfff desktop 3d printers. Tom goddard january 15, 2020 this chimerax tutorial will look at how to visualize atomic models and maps of three conformations of a bacterial atp synthase determined by cryoem at 3. Chimera was designed with extensibility and programmability in mind. If you want to explore chimera further after running through this tutorial, check out the chimera users. Ucsf chimerax tutorials tutorials can be viewed in any browser, but those with clicktoexecute links should be viewed from within chimerax for the links to work.