UCSF Chimera - Revision history

Snehalathak at 06:56, 18 November 2019

2019-11-18T06:56:27Z

Snehalathak at 06:54, 18 November 2019

2019-11-18T06:54:26Z

Snehalathak at 06:51, 18 November 2019

2019-11-18T06:51:10Z

PoojaMoolya at 10:34, 7 May 2019

2019-05-07T10:34:55Z

PoojaMoolya at 06:58, 6 May 2019

2019-05-06T06:58:10Z

PoojaMoolya at 06:58, 6 May 2019

2019-05-06T06:58:00Z

Snehalathak: 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..."

2017-04-28T10:51:14Z

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..."

New page

'''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.

UCSF Chimera version: 1.10.1

Outline:

__TOC__

==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.

@@ Line 18: / Line 18: @@
 ==Basic Level==
 '''1. Overview of UCSF Chimera'''
@@ Line 37: / Line 38: @@
 * Remove the water molecules
 * Add hydrogens
 '''3. Picking and Selection'''
@@ Line 47: / Line 49: @@
 * Open more than one model on the display window
 * Select and move the model
 '''4. Writing Commands'''
@@ Line 58: / Line 61: @@
 * Remove solvent molecules
 * Save the image in different file formats
 '''5. Surface Properties '''
@@ Line 69: / Line 73: @@
 ==Intermediate Level==
 '''6. Build Structures'''
@@ Line 100: / Line 105: @@
 * Color atoms in a protein according to B-factor values
 * Color residues according to kdHydrophobicity values
@@ Line 109: / Line 113: @@
 * Place scenes along a timeline
 * Record  a movie of the resulting animation
 '''11. Axes and Planes'''

← Older revision		Revision as of 06:58, 6 May 2019
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''': Chemistry students	+	'''Learners''': Chemistry students.

← Older revision		Revision as of 06:58, 6 May 2019
Line 7:		Line 7:

	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''': Chemistry students

@@ Line 30: / Line 30: @@
 '''2. Structure Manipulation '''
-* Open a structure on the Chimera window.
+* Open a structure on the Chimera window
-* Download pdb files from PDB database.
+* Download pdb files from PDB database
-* Move, rotate and zoom the structure.
+* Move, rotate and zoom the structure
-* Scale and clip the structure.
+* Scale and clip the structure
-* Change the display using menus in the menu bar.
+* Change the display using menus in the menu bar
-* Remove the water molecules.
+* Remove the water molecules
-* Add hydrogens.
+* Add hydrogens
 '''3. Picking and Selection'''
-* Show labels for atoms and residues.
+* Show labels for atoms and residue.
-* Select atoms and residues using Select menu or by Picking.
+* Select atoms and residues using Select menu or by Picking
-* Change the color and display of the residues.
+* Change the color and display of the residues
 * Add, delete or change atoms
 * 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'''
@@ Line 52: / Line 52: @@
 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
 '''5. Surface Properties '''
-Show surfaces for protein and DNA structures.
+Show surfaces for protein and DNA structures
-* Create images of protein surface colored by :
+* Create images of protein surface colored by:
 (i) Amino acid hydrophobicity
 (ii) Electrostatic Potential
-* Create high quality images for publication using different viewing settings.
+* Create high quality images for publication using different viewing settings
@@ Line 72: / Line 72: @@
 '''6. Build Structures'''
-* Create structures of small molecules, peptides and DNA fragments.
+* Create structures of small molecules, peptides and DNA fragments
-* Modify structure (add and delete atoms).
+* Modify structure (add and delete atoms)
-* Minimize energy.
+* Minimize energy
-* Join models.
+* 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 97: / Line 97: @@
 '''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
@@ Line 105: / Line 105: @@
 '''10. Animation'''
-* Adjust background lighting and effects.
+* Adjust background lighting and effects
-* Create scenes for animation.
+* Create scenes for animation
-* Place scenes along a timeline.
+* Place scenes along a timeline
-* Record  a movie of the resulting
+* Record  a movie of the resulting animation
-* 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

@@ 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.
-'''Learners''': Chemistry students.
+'''Learners''': UG/PG Chemistry students.
-−
 UCSF Chimera version: 1.10.1
 Outline: