Transcript 07-chimera

Structure Visualization
UCSF Chimera
José R. Valverde
CNB/CSIC
[email protected]
© José R. Valverde, 2014
CC-BY-NC-SA
Summary



This is only a short introduction to
visualization of macromolecular structures
using UCSF Chimera
There are many other tools that you can use

PyMOL

RasMol

Jmol

And many, many more...
There are many more things that you can do
with these tools
UCSF Chimera


Interactive molecular graphics program
Built on top of the Python programming
language


Can be extended using Python
Provides

Structure visualization

Volume visualization

Data analysis

Data preparation for other computational tools

Command-line interface for automating tasks
www.cgl.ucsf.edu/chimera

Your first stop for downloads and information
Getting started

Open UCSF Chimera (“chimera”)
Open BPTI

File → Open → Documents/BPTI/4PTI.pdb
Ribbons view

Experiment with the mouse buttons to move,
rotate or zoom/pan the structure
Preset views

Experiment with the various Presets
Preset views

Experiment with the various Presets
Preset views

Experiment with the various Presets
Preset views

Experiment with the various Presets
Preset views

Experiment with the various Presets
Selection: display water

Select → Residue → HOH

Actions → Atoms/Bonds → Show
Note that H atoms are not present in the PDB file
Close the session

File → Close session
Retrieve public data

File → Fetch by ID... → PDB → 1K4R →
Fetch
Build multiscale models

Tools → Higher Order Structure → Mulsticale
Models
Zoom out to see the whole structure of...
Dengue virus
Epsilon/Zeta TA



Close session and
retrieve PDB ID
3Q8X
Select → Structure
→ Ligand
Note that complex
atoms are shown in
wire mode

Ligand

Amino acids
Show ligand (or protein) surface

Select the molecule you want


Select menu
Ctrl+Click on atom and use up/down
arrows


Ctrl-Click → select atom
Up/Down arrow → expand/reduce selection






Residue
Molecule
Ensemble
Model
…
Actions → Surface → Show
Select Active Site

Select → Structure → Ligand

Select → Zone

Actions → Atom/Bonds → Show
Compare two related proteins

File → Fetch by ID... → PDB → 1GVN

Tools → Structure Comparison → MatchMaker
Model Panel

Favorites → Model Panel

Hide (unmark “Shown”) surface and 3Q8X

Hide 1GVN and Show 3Q8X... play
Save selected atoms


Notice that 1GVN does not contain a ligand
After aligning them, we can “transfer” the ligand
from 3Q8X to 1GVN

Select → Selection Mode → Append

Select → Clear selection

Select → Chain → A, B, C, D → 1GVN

Select → Residue → UD1

Actions → WritePDB → Save both models

Save selected atoms only + Save relative to model
3Q8X + File name: 1GVN+UNAG + Save
multiple models in a single file
Verify

Close session and open 1GVN+UNAG.pdb
There is a lot more...

Do not hesitate to check the UCSF Chimera web
site for more information.
mov/subunit.mpeg
The magic garden




You may be wondering where did all those
structures came from....
Open a web browser and go to PDB web site:

www.ebi.ac.uk/pdbe

www.rcsb.org
This is the database repository of known 3D
macromolecular structures.
You can search it... and use the PDB ID to load
structures in Chimera.

File → Fetch by ID
Some interesting entries

309D (DNA)

173D (DNA bound to anticancer drug)

3WN8 (collagen)

3J6R (Human papillomavirus)


Multiscale Model
In the main page, click on “Learn” (left pane) to
see a wealth of educational resources from PDB
(posters, paper models, animations...)
EMDB

http://www.ebi.ac.uk/pdbe/emdb/

This is the Electron Microscopy databank

You can search or browse it, e.g.:

1321 (bacteriophage T7)

6243 (poliovirus)

2240 (human myosin from heart muscle)

… move around.
Questions?
Original picture by muzree, license CC0
http://pixabay.com/en/mosquito-bite-decease-malaria-213806/