Pretty Picture of Calmodulin Kinase I
1) PDB Code 1A06
2) Move things around with the mouse
3) Change the display style using pulldown menus
4) Use presets to change background
5) Overview of command line and Intro to atom-spec
# model
: residue
@ atom
6) Save images
Overlay of Peptides
1) PDB Codes 1MXE and 1YR5
2) Identify appropriate helices and delete the rest using combination of selection and pulldown menus
3) Display residues, delete waters, and color appropriately
4) Overlay structures and explore alignment using MatchMaker
5) Rotate around x axis using command line
6) Manually record and save movie
Morphing Between Apo and Bound Structures
1) PDB Codes 1VFA and 1VFB
2) Overlay structures (using B chain) using MatchMaker
3) Modify display, delete waters, and color appropriately
4) Delete C chain
5) Create morph from apo to bound using Morph Conformations
6) Reopen 1VFB
7) Modify display, delete waters and chains A and B, and color appropriately
8) Manually record and save movie
Electron Density of Open and Closed Structures
1) Download and open 1HGG.pdb and
.
2) Overview of keyboard accelerators
3) Expand map files to cover structure twice using bv and close the original map
4) Focus in on residue of interest, LYS 86, and hide rest and fix background
5) Contour one at 1.0 sigma and make solid and contour the other at 0.3 sigma and make mesh
6) Change transparency of solid contour
7) Save picture
Exercises
1) Recreate the three images needed to produce this folding cycle. Use the structures from pdb codes 1PRW, 1EXR, and 2O5G.
2) I am cowriting a paper with the Ellman lab on designing inhibitors of a M. tuberculosis phosphatase. Below is a draft of one of the figures from the paper. Using these two files--
--recreate the four images needed for this figure. HINT: There are several Chimera Tools that will make your life a lot easier (eg ViewDock and FindHBond).
3) Chimera can, almost literally, make ANY pretty structure picture you can imagine. Go to the image gallery and look through their example images. Pick one that intrigues you and, using what you have learned plus the information provided at the gallery, recreate it. You might also want to check out some of the movies you can make with Chimera at the animation gallery (although the data for these are not provided so you probably won't be able to recreate them).
Making Pretty Pictures
Introduction to Chimera documentation
Overview of pulldown menus
Pretty Picture of Calmodulin Kinase I
1) PDB Code 1A06
2) Move things around with the mouse
3) Change the display style using pulldown menus
4) Use presets to change background
5) Overview of command line and Intro to atom-spec
6) Save images
Overlay of Peptides
1) PDB Codes 1MXE and 1YR5
2) Identify appropriate helices and delete the rest using combination of selection and pulldown menus
3) Display residues, delete waters, and color appropriately
4) Overlay structures and explore alignment using MatchMaker
5) Rotate around x axis using command line
6) Manually record and save movie
Morphing Between Apo and Bound Structures
1) PDB Codes 1VFA and 1VFB
2) Overlay structures (using B chain) using MatchMaker
3) Modify display, delete waters, and color appropriately
4) Delete C chain
5) Create morph from apo to bound using Morph Conformations
6) Reopen 1VFB
7) Modify display, delete waters and chains A and B, and color appropriately
8) Manually record and save movie
Electron Density of Open and Closed Structures
1) Download and open 1HGG.pdb and
2) Overview of keyboard accelerators
3) Expand map files to cover structure twice using bv and close the original map
4) Focus in on residue of interest, LYS 86, and hide rest and fix background
5) Contour one at 1.0 sigma and make solid and contour the other at 0.3 sigma and make mesh
6) Change transparency of solid contour
7) Save picture
Exercises
1) Recreate the three images needed to produce this folding cycle. Use the structures from pdb codes 1PRW, 1EXR, and 2O5G.2) I am cowriting a paper with the Ellman lab on designing inhibitors of a M. tuberculosis phosphatase. Below is a draft of one of the figures from the paper. Using these two files--
3) Chimera can, almost literally, make ANY pretty structure picture you can imagine. Go to the image gallery and look through their example images. Pick one that intrigues you and, using what you have learned plus the information provided at the gallery, recreate it. You might also want to check out some of the movies you can make with Chimera at the animation gallery (although the data for these are not provided so you probably won't be able to recreate them).