Difference between revisions of "UCSF Chimera"

Revision as of 12:28, 6 May 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: Chemistry students

UCSF Chimera version: 1.10.1

Outline:

Basic Level

1. 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.

2. Picking and Selection

• Show labels for atoms and residues.
• 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.

3. 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.

4. 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

5. Build Structures

• Create structures of small molecules, peptides and DNA fragments.
• Modify structure (add and delete atoms).
• Minimize energy.
• Join models.

6. 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.

7. Superimposing and Morphing

• Superimpose and compare different structures of the same protein.
• Morph conformations and create a trajectory.

Advance Level

8. Attributes

• Change attributes of atoms, residues and models.
• Color atoms in a protein according to B-factor values.
• Color residues according to kdHydrophobicity values.

9. Animation

• Adjust background lighting and effects.
• Create scenes for animation.
• Place scenes along a timeline.
• Record a movie of the resulting
• animation.

10. 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.