This is an introduction to molecular docking using autodock vina and ucsf chimera. In the long run it is intended to replace ucsf chimera pettersen et al. The methods enable segmentation, fitting, coarse modeling, measuring and coloring of density maps for elucidating structures of large molecular assemblies such as virus particles, ribosomes, microtubules, and chromosomes. Visualizing density maps with ucsf chimera sciencedirect. Multiscale structural visualization with ucsf chimera. There are also related tutorials at the chimera web site. Ucsf chimera groel visualization the purpose of this exercise is to get familiar with chimera features for density map display, and display of protein data bank pdb models. The mouse preferences contain assignments for a threebutton mouse, but a one or twobutton mouse can also be used. Jul 01, 2014 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. With pychimera you can run scripts depending on chimera from cli with pychimera script. Enable import chimera in interactive coding sessions outside ucsf chimera, including ipython and jupyter notebooks.
Ucsf chimera is a free and open source molecular visualizer. Dragging the mouse in the graphics window lets you rotate, translate, and zoom in on. This tutorial provides an overview of basic features in chimera for displaying and manipulating structures. Ucsf chimera i introduction jeanyves sgro october 10, 2017 contents 1 introduction 2 2 setup 2. Everything should work as expected afterwards for both chimera 1.
Ucsf chimeraa visualization system for exploratory. Chimerausers font size in pulldown menus messages sorted by. The rotation commands also allow you to specify center and axis of rotation it doesnt have to be x, y, or z. Ucsf chimera i introduction jeanyves sgro october 10, 2017 contents 1 introduction 2. Chimerausers rotate a helix elaine meng meng at cgl.
The basics of ucsf chimera this is a very basic introduction to ucsf chimera, a powerful, free software package for visualizing and analyzing macromolecules. Visualizing structures with ucsf chimera for beginners. Ucsf chimera quick reference guide september 2006 commands reverse function. All commands can be truncated to unique strings, but their keywords cannot be truncated except as noted in the. Chimerausers rotating a model by exactly 90 degrees. Ferrin, visualizing density maps with ucsf chimera j struct biol 157. If you have not used chimera before, you can follow the directions included below. The command help can be used to show the manual page for any command. Software extensions to ucsf chimera for interactive visualization of large molecular assemblies by thomas d. I would like to be able to record a movie, based on a chimera script, and have exact framewise control over what is recorded.
Chimera introduction to protein structure bioinformatics 2007 vincent zoete 02232007 121. Chimera movie making university of california, san francisco. We have developed a ucsf chimera tool, rrdistmaps, to compute such. Comparing related structures and viewing the structures in the. Chimera comes preloaded with many helpful tools for analyzing results and making movie files from trajectories. This will force chimera to use your system libraries instead of the ones shipped with chimera. Ucsf chimera quick reference guide march 2003 commands ac enable accelerators keyboard shortcuts alias create an alias or list aliases align align two atoms along the z axis angle measure a bond angle or torsion angle brotation make a bond rotatable cd change the current working directory center center the view on speci. Bmc bioinformatics software tools for integrated sequencestructure analysis with ucsf chimera elaine c meng 0 eric f pettersen 0 gregory s couch 0 conrad c huang 0 thomas e ferrin 0 0 address. Its possible to update the information on ucsf chimera or report it as discontinued, duplicated or spam. Since we cannot wait, well use the fastest setting 1 you will normally use the slowest one 8 select the report threshold poses not scoring within. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality.
We describe methods for interactive visualization and analysis of density maps available in the ucsf chimera molecular modeling package. Visualizing structures with ucsf chimera for beginners chimera basics. View mapping opens a text window showing the alignment between the residues corresponding to alphacarbon atoms in the pdb structure and the residues in the associated sequence. In this tutorial well show how chimera can be used to generate 3d printable molecular models for fdmfff desktop 3d printers. Dear chimera support team, i have a question regarding movie making in chimera. Add a description, image, and links to the ucsf chimera topic page so that developers can more easily learn about it. It addresses challenges in the size, scope, and disparate types of data attendant with cutting. Cootchimera cryoem tutorial march 6th, 2020 description of initial map and model for this tutorial, i have generated a 3. Ucsf chimera getting started dna helix with bound netropsin this tutorial provides an overview of basic features in chimera. Binary yesno contact maps with a single cutoff distance can be generalized to show continuous distance ranges. This introductory course about high quality imaging for publication will make use of the free.
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. You can interact with chimera by using the menus andor by entering commands. Dear masaki, you can delete all the bonds with command. Chimera biochemistry computational research facility.
Tools for integrated sequencestructure analysis with ucsf. Learn the basic functionality of ucsf chimera, such as loading pdb coordinates into the software, manipulating the structure in 3d, and saving your session. Select the precision click on advanced options select the number of binding modes to generate 9 select the thoroughness of the search. The design, implementation, and capabilities of an extensible visualization system, ucsf chimera, are discussed. For a quick workaround, go into opt ucsf chimera lib and delete all instances of libfreetype and libz. Aug 23, 2018 ucsf chimera was added by stephanf in aug 2016 and the latest update was made in apr 2020. Chimera quick reference guide pdf includes a list of commands and. 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 images and animations suitable for publication and presentation. Ucsf chimera quick reference guide october 2002 midas emulator commands ac enable accelerators keyboard shortcuts alias create an alias or list aliases align align two atoms along the z axis angle measure a bond angle or torsion angle brotation make a bond rotatable cd change the current working directory center center the view on speci. Ucsf chimera is a highly extensible, interactive molecular visualization and analysis system.
If you want to explore chimera further after running through this tutorial, check out the chimera users. Contact maps are a convenient method for the structural biologists to identify structural features through twodimensional simplification. If you are familiar with the ucsf chimera software, skip through exercises 1 just make sure that you visualize the hiv1 reverse transcriptase protein pdb entry 3v4i in complex with dna and a nucleoside inhibitor azt before attempting the challenge question. The jalview chimera view window has up to five menus. Ucsf chimera software manual guide to make a protein fusion. Past commands can be accessed from the command history, and commands can be placed in an executable command file.
To make a movie, you will also need to download a script for writing trajectory files that chimera can read. Chimera users how to connect two proteins next message. The software is ed and licensed by the regents of the university of california. 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. I would like to fuse two proteins in ucsf chimera that were both loaded from a pdb file from the pdb database in chimera. Chimera commands are listed below and in the quick reference pdf. Chimera users how to connect two proteins elaine meng meng at cgl. 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.
I notice that some actions in chimera can be undid, such as undo selection or undo move. Turn is the same as roll except for the default number of frames. Ucsf chimera getting started dna helix with bound netropsin this tutorial provides an overview of basic features in chimera for displaying and manipulating structures. The software is ed and licensed by the regents of the univer sity of california. Visualizing molecular simulations che210d overview. Dec 04, 2014 learn the basic functionality of ucsf chimera, such as loading pdb coordinates into the software, manipulating the structure in 3d, and saving your session. Highquality images and animations can be generated. Coot chimera cryoem tutorial march 6th, 2020 description of initial map and model for this tutorial, i have generated a 3. Sets the center of rotation based on the selected atoms without adjusting the view. You can interact with chimera using menus andor commands. Ucsf chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. Ucsf chimera was developed by the computer graphics laboratory at the university of california, san francisco, under support of nih grant p41rr01081. Software extensions to ucsf chimera for interactive.
Commands index university of california, san francisco. Chimera seems to make a funny distinction between internal trajectory frames and movie frames which i dont get. Describe why you think phenotypes may come out in mixed cell competitive situations which may not be apparent in 100% knockout situations. All commands can be truncated to unique strings, but their keywords cannot be truncated except as noted in the documentation. Structures such as ribosomes, virus capsids, molecular motors, cytoskeletal filaments, proteasomes, nucleosomes, chaperonins, transmembrane channels, and pumps, composed of tens to thousands of macromolecules, have been determined to atomic resolution.
Tom goddard, programmeranalyst, resource for biocomputing, visualization, and informatics, ucsf host. If you are familiar with the ucsf chimera software, skip through exercises 1 and 2 just make sure that you visualize the mhctcr complex pdb entry 1fyt and antibody structures pdb entries 1igt, and 3hfm before attempting the challenge question. The same movement when performed far from the molecule, e. Yes, turn or roll specifies exact rotations, move exact translations. Chimera includes complete documentation and is free of charge for academic, government, nonprofit, and personal use. 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. Computer graphics laboratory, university of california san francisco, 600 16th street, san francisco, ca 941432440, usa background. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. This is a nifty mixed chimera approach which sets up a competitive situation between the wt versus wasp l272p and i296t neutrophils. Chimera users rotate a helix elaine meng meng at cgl. 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. Ucsf chimera an extensible molecular modeling system chimera is an extensible interactive 3d modeling system designed to allow developers to quickly incorporate novel visualization algorithms and analysis tools chimera runs on laptopsdesktops and takes maximum advantage of lowcost, stateoftheart graphics chips. Advances in electron cryomicroscopy and xray crystallography have enabled structures of many cellular machines to be determined.
Users of the mac x11 version of chimera, see below. A mouse or touchpad trackpad can be used to manipulate the view of structures and other 3dimensional data in the chimera graphics window. In the section below we will turn on the linecommand. Molecular docking using autodock vina and ucsf chimera. Presentation of chimera this introductory course about 3d structure visualization and high quality imaging for publication will make use of the free program chimera.
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