Download 07-chimera

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