UCSF-Chimera/C4/Attributes/English

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Attributes.
Slide Number 2 Learning Objectives	In this tutorial we will learn to, Change attributes of atoms, residues and models. Color atoms in a protein according to B-factor values. Color residues according to kdhydrophobicity values.
Slide Number 3 Pre-requisites	To follow this tutorial you should be familiar with, Chimera interface If not, for relevant tutorials, please visit our website.
Slide Number 4 System Requirement	To record this tutorial I am using Ubuntu OS version. 14.04 Chimera version 1.10.2 Mozilla Firefox browser 42.0 And a working Internet connection.
Double-click on the Chimera icon present on the desk top. Type, open 1zik Press enter.	Here I have opened the Chimera window. Using command line open the structure of Leucine zipper. On the command text box, type, open 1zik Press enter.
Cursor on the panel. Click on Presets menu, click on Interactive 2.	The model on the panel is shown as ribbons. Using Presets menu, change the display to Interactive 2 .
On the command line type, delete solvent. Press enter.	To hide water molecules, on the command line type, delete solvent. Press enter.
On the command line type, rep sticks Press enter	Change the display to sticks, type, rep stick
On the command line type, addh , Press enter.	Add hydrogens to the structure, type, addh
Cursor on the panel.	Now let us learn how to change the attributes of atoms and residues for this structure.
Slide Number 5 Attributes	Attributes are properties with names and values. In Chimera, items such as atoms, bonds, residues and molecule models have Attributes.
Cursor on the panel.	There are different ways to change the Attributes.
Click on the Favorites menu, scroll down and click on Model Panel.	Open the Model Panel using Favorites menu.
Cursor on the Model Panel dialog box. Click on “attributes” button on the right side of the panel.	A Model Panel dialog box appears on the screen. Click on the attributes button on the right side of the panel.
Cursor on the 1zik Attributes dialog box. Click on Molecule Attributes button.	A Attributes dialog box for 1zik opens on the screen. The dialog box has attribute list.
Cursor on the panel. Click on Molecule Attributes	The list includes. Molecule Attributes and its components, Atom, bond and residue attributes. Select Molecule Attributes.
Cursor on the dialog box. Click on Molecule Attributes.	The available attributes are listed on the window.
click on aromatic display button. Select True from the drop-down menu.	For example to change the display of aromatic rings; Click on the button next to aromatic display. Select True from the drop-down.
Click on Disk in the Aromatic ring style option.	Select Aromatic ring style as disk. Click on the color well next to aromatic color. Select color from the color editor. Close the dialog box.
Zoom the structure. Cursor on Aromatic rings.	Observe the panel. All the aromatic rings are shown with disks in the center.
Type, rep bs Press enter.	Change the display of the structure to ball and stick. On the command line, type, rep bs Press enter.
Change the ball scale value to 0.5.	On the attributes dialog box, change the Van der Walls radii of the atoms. Change the value of ball scale to 0.5. press enter.
Cursor on the panel.	Observe the panel. The atoms are shown with larger atomic radii.
Click on Atom Attributes.	Again click on Molecular Attributes check box. From the list, click on Component Atom Attributes.
Select sphere.	In the corresponding window, click on atom style button . The drop-down menu has many options. Click on sphere to change the display to cpk. Observe the panel. Select dot to bring back the sticks display.
Click on Component Bond Attributes.	Now click on Component Bond Attributes. Here there are options to change bond style.
Click on Component Residue Attributes.	Click on Component Residue Attributes. Here we have options to change the attributes of the ribbon.
Click on Presets menu, change the display to ribbons.	Using presets menu, change the display of the structure on the panel to ribbons.
Click on the color well. Choose a color from the color editor dialog box. Close the color editor dialog box.	Now, In the Attribute dialog box, Click on the color well next to ribbon color. Select a ribbon color, and click on close option to close the color editor.
Click on ribbon cross-section select edged from the options.	There are options to change the cross-section of the ribbon and scaling. Close the dialog box.
Click on Presets menu, select Interactive 2 option.	Again change the display to atoms using Presets menu.
Cursor on Tools menu.	Attributes can also be changed using Tools menu.
Scroll down the Tools menu, select Structure Analysis option. From the sub-menu select Render by Attribute.	Click on tools menu, scroll down to Structure Analysis. And select Render by Attribute option from the sub-menu.
Cursor on the dialog box.	A Render by attribute dialog box opens.
Cursor on Render by attribute dialog box. Click on atoms from the Attributes drop-down.	Here we have options to change the attributes of atoms, residues, molecules, segmentation regions etc. Select atoms. Click on Render.
Click on the the Attribute list.	Click on Attribute list to check for the available options. The list shows two options; bfactor and occupancy These two attributes can be read from the input PDB file.
Select bfactor. Cursor on the Histogram.	Choose bfactor. A histogram of values will appear, with colored vertical bars.
Slide Number 6 B-factor	B-factor values are a measure of mobility in the macromolecule. Atoms with low B-factor values belong to a part of the structure that is well ordered. Atoms with large B-factor values belong to part of the structure that is very flexible.
Slide Number 7 B-factor	PDB file for a protein structure contains B-factor information.
Drag the vertical bars on histogram using mouse. Cursor on the Value text box. Drag the blue vertical bar to zero, red to 100. Fix the white bar at value 50.	Back to the panel. The vertical bars can be dragged along the histogram with the mouse. The Value of B-factor is displayed in the Value text box. Drag the blue vertical bar to zero, red to 100. Then fix the white bar at value 50.
Cursor on the panel. Click on colors option. Click on color atoms, keep opaque and color surfaces.	There are 3 options to display the structure according to B-factor value; colors, radii or worms. Click on Colors. Check options for color atoms, keep opaque and color surfaces. The default color palette is blue and red. You can change the color palette, if you wish to change the colors.
Click Apply.	Click Apply button.
Cursor on the panel.	Observe the panel. Atoms with high B-factor values are shown in red and least in blue.
Cursor on the panel.	As expected atoms with higher B-factors are on the outside of the structure.
Cursor on the panel.	Now let us change the attributes of Residues.
Select residues in the attributes drop-down in the Render dialog box.	In the Attribute dialog box, click on Attributes button. From the drop-down, select residues.
Cursor on the panel.	Select Render. The attributes for residues include kdHydrophobicity scale.
Select kdHydrophobicity .	Select kdHydrophobicity from the drop-down menu. The values are displayed in the histogram.
Slide Number 8 kdHydrophobicity	kdHydrophobicity scales are values that define relative hydrophobicity of amino acid residues. KdHydrophobicity values are positive for hydrophobic residues and Negative values for polar residues.
Cursor on the panel.	Hydrophobicity of the residues can be shown with colors or with worms. Choose Colors. By default some of the parameters are selected. Click on Apply button. observe the panel. The hydrophobic residues are colored in red, and hydrophilic residues are colored in blue.
Click on Worms option. Click on apply.	Click on Worms, Click on Apply. Observe the panel. Worms are modified ribbons that vary in radius.
Cursor on the panel.	The most hydrophobic residues face the interior of the structure.
Cursor on the panel.	By default, the more hydrophobic residues will be shown with larger radius.
Click on worm style to non-worm. Click on OK.	To return to normal ribbon instead of worm; Click on the worm-style button and choose non-worm. Click on OK button.
Click on File menu, scroll down and click on Close Session option.	Close the Chimera session using File menu.
Slide Number 9 Summary	Let's summarize, In this tutorial we have learnt to, Change attributes of atoms, residues and models. Color atoms in a protein according to B-factor values. Color residues according to kdHydrophobicity values.
Slide Number 10 Assignment	As an Assignment, Open a model of hemoglobin (PDB code: 2HCO) on the panel. Color the atoms according to B-factor values. Color the residues according to the kdHydrophobicity values.
Slide Number 11 Acknowledgement	* This video summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.
Slide Number 12	* We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
Slide number 13	The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
	This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak