Ucsf chimera was developed by the computer graphics laboratory at the university of california, san francisco, under support of nih grant p41rr01081. Ucsf chimerax user guide ucsf chimerax is the successor program to ucsf chimera. It can be used as a helper application for several types of files linked to web pages. Analysis of large assemblies requires the same tools to study many local regions in atomic detail. Set the map to an appropriate threshold using the volume viewer 0. Ucsf chimera groel visualization the purpose of this exercise is to get familiar. The content for this manual is part of the lammps distribution. This is a recording of a virtual workshop on manual buildingrefinement of atomic models in to cryoem density maps, using ucsf chimera for initial fitting and coot 0. Ucsf chimera is developed by the resource for biocomputing, visualization, and informatics rbvi at the university of california, san francisco, funded by the national institutes of health nigms p41gm103311. Lab manual ucsf lab manual ucsf recognizing the exaggeration ways to get this book lab manual ucsf is additionally useful. 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. Visualizing density maps with ucsf chimera request pdf. All submenus sections are grouped on this page to provide a list of all tutorials. Chimera assembles a new 3d module automatically if a perfect match of module ends is found in the 3d model.
Ucsf chimera getting started dna helix with bound netropsin this tutorial provides an overview of basic features in chimera. Chimera quick reference guide pdf includes a list of commands and several examples of commandline atom specification. Many of the functions you will be using are experimental or under development. You can interact with chimera using menus andor commands. Proteinligand docking with pyrx university of missouri. You can build a local copy of the manual as html pages or a pdf file, by following the steps on the manual build doc page. With pychimera you can run scripts depending on chimera from cli with pychimera script. 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. An introduction to molecular visualization with ucsf chimera. Therefore, visualization software, used to set up calcula tions, assess. What are the computer requirements to run ucsf chimera and. Ucsf uniform guidance workgroup assessment report update on ucsf actions and outputs 42916 page 1 ucsf.
Chimera quick reference guide pdf includes a list of commands and several examples of commandline atom specification introduction to pdb format describes types and formats of data commonly found in pdb files. Explore 5 apps like ucsf chimera, all suggested and ranked by the alternativeto user community. Ucsf chimera is a powerful, well engineered, molecular graphics package with a large number of functions that is under ongoing development and maintenance. In this tutorial well show how chimera can be used to generate 3d printable molecular models for fdmfff desktop 3d printers. It is intended to give an overview of the ideas which form the basis of the dock suite of programs and to detail the available user parameters. Software extensions to ucsf chimera for interactive.
The basics of ucsf chimera this is a very basic introduction to ucsf chimera, a powerful, free software package for visualizing and analyzing macromolecules. Exercise 1 loading a structure into chimera two methods can be used to load a structure into chimera. In this case, ab initio model generation converged on the model with inverted hand, so we need to flip the map. It is one of a number of freely available tools to visualize and manipulate threedimensional molecular datasets, but it stands out due to its rich features, the versatility of its use and the ease with which common tasks can be. Basic functions general usage topics, including commands tools descriptions of the chimera tools menu entries. These include working with the embedded jmol molecular structure viewer or ucsf chimera, building and viewing trees and principal components analysis pca plots, and using. Alternatively, some universities have computer clusters that run ucsf chimera and maybe pymol that students have access to which will be significantly more powerful than any computer you can build. If you want to explore chimera further after running through this tutorial, check out the chimera users. The chimera users guide has three main parts, which are interconnected. Take a close look at the helices you should notice that they are left handed. Tutorials exercises ranging from beginnerlevel to more advanced.
Ucsf chimera is a free and open source molecular visualizer. Ucsf chimeraa visualization system for exploratory. With more than 20 locations throughout san francisco and beyond, uc san francisco is an industry of its own, contributing greatly to the intellectual vigor and. The downside is you have to queue your work on the cluster and there could be long waits especially if the clusters are used for other things. So, you may have to install the latest version of the program on your machine at home or in the classrom. Ucsf chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. For the arp23 system, running multifit with global sampling gave correlation scores for the top ten solutions ranging from 0. These initial placements can come from individual subunit fitting using, for example, the chimera fit in map tool, manual visual fitting, or other methods based on prior knowledge of the complex. If chimera is installed in usrlocalchimera, then you run. Results can be exported to other software programs like ucsf chimera or pymol for analysis. Hi all, i am a new user of chimera and need to quickly prepare an image in which the hypervariable. 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 provides an overview of basic features in chimera for displaying and manipulating structures. Artists like abidar, she added, have every right to escape to safety. Ucsf chimeraa visualization system for exploratory research and analysis. Tools descriptions of the chimera tools menu entries. You have remained in right site to start getting this info. The software is ed and licensed by the regents of the university of california. Popular alternatives to ucsf chimera for windows, mac, linux, wine, software as a service saas and more. Moroccans protest royal pardon of spanish pedophile thousands of moroccans protested the decision to free a pedophile convicted of filming and raping children. The chimera quick reference guide pdf summarizes commandline usage chimera documentation, including the users guide, is bundled. Chimera includes complete documentation and can be downloaded free of. Chimera is an interactive molecular graphics program developed by the computer graphics lab at ucsf.
Ucsf chimera is a highly extensible, interactive molecular visualization and analysis system. How to install ucsf chimera in linux welcome to jean. This section is intended as a reference manual for the features of the dock suite of programs. Pettersen ef1, goddard td, huang cc, couch gs, greenblatt dm, meng ec, ferrin te. This is the result of our collaboration with the group of san francisco. Chimera includes complete documentation and several tutorials, and can be downloaded. Basic functions general usage topics, including commands. Useful chimera modulesfunctions molecular measurements chimera module functions use points, which are returned by atoms coord or xformcoord methods distance sqdistance.
Working with menus, part 1 manipulation, selection, and chains ucsf chimera with 1zik getting started on linux, run the executable chimera in the bin directory of your chimera installation. The ucsf uniform guidance workgroup has been working alongside the ucop system wide system task force to evaluate policies and procedures in the guidelines and its appropriate implementation system wide and at ucsf. Data sets and the most recent version of this tutorial html, pdf are online. You could buy guide lab manual ucsf or acquire it as soon as feasible. Ucsf chimera is a highly extensible, interactive molecular visualization. An andrej sali lab ucsf chimera, modeller, and imp.
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. Highquality images and animations can be generated. Chimera can read molecular structures and associated data in a large number of formats, display the structures in a variety of representations, and generate highquality. Ucsf chimerax or simply chimerax is the nextgeneration molecular. Chimera manual help buttons session saving more tutorials starting chimera on linux run the executable chimera in the bin directory of your chimera installation. If you have already installed the chimera program from. Chimera includes complete documentation and is free of charge for academic, government, nonprofit, and personal use. Chimerax builds on our highly successful ucsf chimera visualization. The c6 reconstruction was segmented in ucsf chimera goddard et al. More tutorialsare available at the chimera website.
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