Difference between revisions of "UCSF-Chimera/C3/Superimposing-and-Morphing/English-timed"

| Welcome to this tutorial on '''Superimposing and Morphing'''

| In this tutorial, we will learn to : '''Superimpose''' and compare different structures of the same protein.

| Morph '''conformations''' and create a '''trajectory'''.

| To follow this tutorial you should be familiar with, '''Chimera''' Interface.

| Here 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''' window.

| The structure of '''Squalin Synthase''' opens on the screen.

|Now let us prepare this structure for '''superimposing'''.

| It contains two copies of the same '''protein'''.

|Using the '''command line''' delete one of the chains.  

| I will recall the command by clicking on the command history.

| From the command history dialog box, select the command '''“delete:.a”'''  

| Next, to remove '''solvent '''molecules from the structure; I will select the command “'''del solvent'''”. Press '''Enter'''.

| This structure is bound to the substrate analog '''Farnesyl thiopyrophosphate'''. '''FPS''' in short.

|For this we will fetch a structure of the same enzyme without substrate.

| On the '''command line''' type “'''open 2zco'''” press enter.

| Now these two structures are ready to be '''superimposed'''.

| '''Superimposition or Structural alignment''' is a tool to compare two or more '''protein''' structures.

|The alignment is based on their shape and three-dimensional conformation.

| Before we start '''superimposing''', let us place some icons in the tool bar.  

| Click on '''Favorites menu.'''

|'''Scroll down to Add to favorites/Tool bar '''option.

| Check boxes for, '''Command line''' , '''Model Panel''' , '''Side View'''.

| Scroll down and click on, '''MatchMaker '''  and '''Match-Align'''

|Select tools according to your requirement.

| Observe the panel.  

| Now let us '''superimpose''' the structures using '''MatchMaker''' function.

|For now, let us continue with the default settings. Press '''OK''' button.  

|The two structures are '''superimposed''' on each other.

| The two structures are almost completely '''superimposable''' with each other.

|Except for a small part which is '''non-superimposable'''.

| The fragment involved in this '''non-superimposable''' part starts from : The '''amino acid''' number 53 to '''amino acid''' number 57.

| To select the chains, click on their '''pdb Ids'''.

| In this box the '''amino acid '''pairs used in the final fit, are shown with light orange boxes.

| The structures are mostly similar except for the loop at residues 52-54.

| This corresponds to the '''non-superimposable''' part of the structure.

| You can change the color of this '''non-superimposing''' parts using '''Actions''' menu.

| Now, let me demonstrate how to morph '''conformations''' and create a trajectory.

| '''Morphing''' involves calculating a series of intermediate structures between the original input structures.

| The series of intermediate structures created can be saved as '''Molecular Dynamics Movie.'''- in short''' MD Movie.'''

| Click on '''Tools menu scroll down to Structure Comparison.'''

| '''Click on Morph conformations '''option.

| In the resulting list of the models dialog box; double click on model number zero, that is '''3w7f''' to add to the conformations.

| Next click on model number 1 that is '''2zco'''.

| This sequence corresponds to : a morph '''trajectory''' from ligand , bound to the structure to empty structure ,  and then back.

| After a few seconds a''' MD Movie''' is created.  

| The dialog box has buttons to play or pause the movie.

| Now let's summarize what we have learnt.

| In this tutorial we have learnt to, '''Superimpose '''and compare different structures of the same protein.

| Morph '''conformations''' and create a '''trajectory'''.

| Save the trajectory as '''Molecular Dynamics Movie.'''

| For the assignment, Open the structures of '''GTP binding '''proteins with the '''PDB code''': '''1TAG''' and '''1TND'''

| Superimpose the structures using '''MatchMaker''' tool.  

| The '''Spoken Tutorial Project''' Team conducts workshops and  gives certificates for those who pass an online test.  For more details, please write to us.  

| '''Spoken Tutorial Project''' is funded by '''NMEICT, MHRD, Government of India. '''More information on this '''Mission''' is available at the link shown

| This is '''Snehalatha''' from '''IIT Bombay''' signing off. Thank you for joining.