Difference between revisions of "UCSF-Chimera/C3/Build-Structures/English-timed"

| | In this tutorial, we will learn to :Create structures of small molecules, '''peptides''' <br/> and '''DNA''' fragments.

| |  Modify structure. Minimize energy, and Join models

| | To follow this tutorial you should be familiar with, '''Chimera Interface''' , If not, for relevant tutorials, please visit our website.  

| | 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.

| | Here I have opened a '''Chimera graphics window.'''  

| | A '''Build Structure''' dialog box opens on the screen.

| | Click '''Start Structure''' button available at the top of the dialog box.

| | We can also modify existing structure, adjust bonds, adjust torsions, join models etc.  

| | We can add '''atom''', '''fragment''', fetch a structure from '''Pubchem''' data base.

| | Create '''peptide''', '''DNA''', '''RNA''' etc.  

| | To build small molecules, click on '''atom '''radio button. '''Atom parameters''' section opens.

| | By default the structure begins with a '''helium''' atom.

| | Click on '''Center of the view''' radio button, to place the '''helium''' atom at the center of the panel.

| | In '''named''' text box type the name of the session as  '''Sample1'''.  

| | In the '''Build Structure''' dialog box;

| | Change the element to '''carbon''', '''bonds''' to 4 and geometry to '''tetrahedral'''.

| | Hydrogens are attached as needed to satisfy the valency.

| | By default some of the parameters are already selected, leave them as such.

| | Using '''Select''' menu clear the selection.

| | In the '''Modify Structure''' dialog box; Change the element to '''nitrogen''', '''bonds''' to 3 , geometry '''trigonal'''.

| | Click on '''Apply button.'''

| | If you want to delete any atom or bond from the structure; Select the atom or the bond, click on '''delete''' button in the '''Build Structure''' dialog box.

| | Using the center mouse button, drag and place this model at the corner of the panel.

| | In Build Structure dialog box; Click the drop-down menu and select '''Start Structure option.'''

| | Now click on '''fragment '''radio''' '''button'''.'''

| | A Fragment library of various '''cyclic '''compounds is listed here.

| | Click on 5-membered rings.

| | Choose fragment from the list.

| | Click on '''Apply button'''

| | Uncheck the box for '''model number zero''' on the '''Active model''' status bar.

| | Using center mouse button move the '''imidazole''' closer to the '''amine model'''.

| We can join the two models on the panel; Using '''Join Models''' option in the Build structure dialog box.

| | Select one '''hydrogen''' atom from each model where you intend to form a bond.

| | Hold''' CTRL''' and '''Shift''' key at the sametime click on the hydrogen.

| | Now the '''hydrogen'''s are selected.

| | Click on '''Apply button.'''

| | Close the '''session '''using''' File '''menu'''.'''

| | Click on the '''lighting bolt icon''' at the bottom of the window; to get back to '''graphics''' window.

| | Next let us create a '''peptide''' chain.  

| | Click on '''peptide '''radio button'''.'''

| | In the '''Peptide''' '''Sequence''' text box, type the single letter code for amino acids.

| | Let us type some random amino acid sequence.  

| | Type, '''ACDEFGH''' The residues are added from N to C terminus.

| | '''Add Peptide Sequence '''dialog-box''' '''opens.

| | By default '''phi''' and '''psi''' angles of -57 and -47 are displayed.

| | These values correspond to a '''alpha-helix '''structure''' '''for the peptide fragment'''.'''

| | For now we will leave the phi\psi values unchanged.

| | Click on OK button.

| | To minimize energy of the structure, type '''minimize''' on the '''command text box''' Press enter.  

| | By default some parameters are selected.

| | For now we will not make any changes. Click on '''OK''' button.

| | Observe the panel, hydrogens are added to the structure.

| | Another dialog box opens, choose the force field package.

| | By default '''AMBER ff14SB''' is selected for standard residues.

| | Now on the panel we have a structure with most preferred conformation.  

| | Close the session using '''File '''menu and Open '''Graphics''' window.

| | Using the '''Build stucture''' tool, we can create a double helical DNA/RNA.  

| | In the '''Sequence''' text box, type one letter '''nucleotide code for a DNA fragment.'''

| | Edit the name as '''Sample3'''

| | Change to atoms display using presets menu.

| | Let's summarize, In this tutorial we have learnt to, Create structures of small molecules, peptides <br/> and '''DNA''' fragments.

| | Modify structure.

| |  Minimize energy, and  Join models.

| | For the Assignment, Join two '''benzene''' molecules to build a '''biphenyl molecule'''.

| |  This video summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.

| | The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India.  

| | This is Snehalatha from IIT Bombay signing off.