Difference between revisions of "UCSF Chimera"
From Script | Spoken-Tutorial
Snehalathak (Talk | contribs) (Created page with "'''UCSF Chimera''' UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, su...") |
Snehalathak (Talk | contribs) |
||
| (5 intermediate revisions by 2 users not shown) | |||
| Line 8: | Line 8: | ||
The Spoken Tutorial Effort for UCSF Chimera has being contributed by Dr. Snehalatha Kaliappan with domain reviews done by faculty and research scholars from the Chem Engg Dept, IIT Bombay. | The Spoken Tutorial Effort for UCSF Chimera has being contributed by Dr. Snehalatha Kaliappan with domain reviews done by faculty and research scholars from the Chem Engg Dept, IIT Bombay. | ||
| + | '''Learners''': UG/PG Chemistry students. | ||
UCSF Chimera version: 1.10.1 | UCSF Chimera version: 1.10.1 | ||
Outline: | Outline: | ||
| − | |||
| Line 19: | Line 19: | ||
==Basic Level== | ==Basic Level== | ||
| − | |||
| − | + | '''1. Overview of UCSF Chimera''' | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | * About UCSF Chimera | |
| + | * Download and installation of UCSF Chimera on Ubuntu Linux OS | ||
| + | * Chimera interface, Menu bar | ||
| + | * Uses and Advantages | ||
| + | * Play video clippings of Chimera available on our website | ||
| − | * Show labels for atoms and | + | |
| − | * Select atoms and residues using Select menu or by Picking | + | '''2. Structure Manipulation ''' |
| − | * Change the color and display of the residues | + | |
| + | * Open a structure on the Chimera window | ||
| + | * Download pdb files from PDB database | ||
| + | * Move, rotate and zoom the structure | ||
| + | * Scale and clip the structure | ||
| + | * Change the display using menus in the menu bar | ||
| + | * Remove the water molecules | ||
| + | * Add hydrogens | ||
| + | |||
| + | |||
| + | '''3. Picking and Selection''' | ||
| + | |||
| + | * Show labels for atoms and residue. | ||
| + | * Select atoms and residues using Select menu or by Picking | ||
| + | * Change the color and display of the residues | ||
* Add, delete or change atoms | * Add, delete or change atoms | ||
* Rotate bonds | * Rotate bonds | ||
| − | * Open more than one model on the display window | + | * Open more than one model on the display window |
| − | * Select and move the model | + | * Select and move the model |
| − | ''' | + | |
| + | '''4. Writing Commands''' | ||
Type commands to, | Type commands to, | ||
| − | * Change the display to atoms | + | * Change the display to atoms |
| − | * Show and hide ribbons | + | * Show and hide ribbons |
| − | * Change the color of the amino acid residues | + | * Change the color of the amino acid residues |
| − | * Label individual residues | + | * Label individual residues |
| − | * Remove solvent molecules | + | * Remove solvent molecules |
| − | * Save the image in different file formats | + | * Save the image in different file formats |
| − | |||
| − | Show surfaces for protein and DNA structures | + | '''5. Surface Properties ''' |
| − | * Create images of protein surface colored by : | + | |
| + | Show surfaces for protein and DNA structures | ||
| + | * Create images of protein surface colored by: | ||
(i) Amino acid hydrophobicity | (i) Amino acid hydrophobicity | ||
(ii) Electrostatic Potential | (ii) Electrostatic Potential | ||
| − | * Create high quality images for publication using different viewing settings | + | * Create high quality images for publication using different viewing settings |
==Intermediate Level== | ==Intermediate Level== | ||
| − | |||
| − | * Create structures of small molecules, peptides and DNA fragments | + | '''6. Build Structures''' |
| − | * Modify structure (add and delete atoms) | + | |
| − | * Minimize energy | + | * Create structures of small molecules, peptides and DNA fragments |
| − | * Join models | + | * Modify structure (add and delete atoms) |
| + | * Minimize energy | ||
| + | * Join models | ||
| − | ''' | + | '''7. Structure Analysis''' |
| − | * Measure distance between atoms in the structure | + | * Measure distance between atoms in the structure |
| − | * Show hydrogen bonds | + | * Show hydrogen bonds |
| − | * Identify non-polar interactions | + | * Identify non-polar interactions |
| − | * Rotate bonds in the residues to get different rotamers | + | * Rotate bonds in the residues to get different rotamers |
| − | ''' | + | '''8. Superimposing and Morphing''' |
| − | * Superimpose and compare different structures of the same protein | + | * Superimpose and compare different structures of the same protein |
| − | * Morph conformations and create a trajectory | + | * Morph conformations and create a trajectory |
| Line 86: | Line 100: | ||
| − | ''' | + | '''9. Attributes''' |
| − | * Change attributes of atoms, residues and models | + | * Change attributes of atoms, residues and models |
| − | * Color atoms in a protein according to B-factor values | + | * Color atoms in a protein according to B-factor values |
| − | * Color residues according to kdHydrophobicity values | + | * Color residues according to kdHydrophobicity values |
| + | '''10. Animation''' | ||
| − | + | * Adjust background lighting and effects | |
| + | * Create scenes for animation | ||
| + | * Place scenes along a timeline | ||
| + | * Record a movie of the resulting animation | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | ''' | + | '''11. Axes and Planes''' |
| − | * Show Axes, Planes and Centroids for structure of Green Fluorescent Protein | + | * Show Axes, Planes and Centroids for structure of Green Fluorescent Protein |
| − | * Show 2D-Labels | + | * Show 2D-Labels |
| − | * Draw Arrows | + | * Draw Arrows |
| − | * Clip a model of Myoglobin using Per-Model clipping tool | + | * Clip a model of Myoglobin using Per-Model clipping tool |
Latest revision as of 12:26, 18 November 2019
UCSF Chimera
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. High-quality images and animations can be generated.
Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics, funded by the National Institutes of Health (NIGMS P41-GM103311). UCSF Chimera is licensed for noncommercial use at no cost by the Regents of the University of California. You must agree to the terms and conditions of use as specified in the license agreement before you will be permitted to download Chimera.
The Spoken Tutorial Effort for UCSF Chimera has being contributed by Dr. Snehalatha Kaliappan with domain reviews done by faculty and research scholars from the Chem Engg Dept, IIT Bombay.
Learners: UG/PG Chemistry students.
UCSF Chimera version: 1.10.1
Outline:
Basic Level
1. Overview of UCSF Chimera
- About UCSF Chimera
- Download and installation of UCSF Chimera on Ubuntu Linux OS
- Chimera interface, Menu bar
- Uses and Advantages
- Play video clippings of Chimera available on our website
2. Structure Manipulation
- Open a structure on the Chimera window
- Download pdb files from PDB database
- Move, rotate and zoom the structure
- Scale and clip the structure
- Change the display using menus in the menu bar
- Remove the water molecules
- Add hydrogens
3. Picking and Selection
- Show labels for atoms and residue.
- Select atoms and residues using Select menu or by Picking
- Change the color and display of the residues
- Add, delete or change atoms
- Rotate bonds
- Open more than one model on the display window
- Select and move the model
4. Writing Commands
Type commands to,
- Change the display to atoms
- Show and hide ribbons
- Change the color of the amino acid residues
- Label individual residues
- Remove solvent molecules
- Save the image in different file formats
5. Surface Properties
Show surfaces for protein and DNA structures
- Create images of protein surface colored by:
(i) Amino acid hydrophobicity (ii) Electrostatic Potential
- Create high quality images for publication using different viewing settings
Intermediate Level
6. Build Structures
- Create structures of small molecules, peptides and DNA fragments
- Modify structure (add and delete atoms)
- Minimize energy
- Join models
7. Structure Analysis
- Measure distance between atoms in the structure
- Show hydrogen bonds
- Identify non-polar interactions
- Rotate bonds in the residues to get different rotamers
8. Superimposing and Morphing
- Superimpose and compare different structures of the same protein
- Morph conformations and create a trajectory
Advance Level
9. Attributes
- Change attributes of atoms, residues and models
- Color atoms in a protein according to B-factor values
- Color residues according to kdHydrophobicity values
10. Animation
- Adjust background lighting and effects
- Create scenes for animation
- Place scenes along a timeline
- Record a movie of the resulting animation
11. Axes and Planes
- Show Axes, Planes and Centroids for structure of Green Fluorescent Protein
- Show 2D-Labels
- Draw Arrows
- Clip a model of Myoglobin using Per-Model clipping tool
