Chimera2 Quick Start Guide

August 28, 2015

Chimera2 is the next generation visualization program from the Computer Graphics Lab at UC San Francisco, following Midas, MidasPlus, and Chimera 1.

Features

Chimera2 has better graphics (e.g. interactive ambient shadows), handles large structures (millions of atoms) much faster, and has a modern single window user interface, and will have a web site of available extensions written by others using documented programming interfaces.

Compatibility

Chimera2 is not backward compatible with Chimera 1, although many aspects will be familiar from Chimera 1.

Initial Release in December 2015

We plan an initial release with basic capabilities at the end of 2015, on Mac (10.10 or newer) and Linux computers. A Windows release will be later in 2016.

Example Atomic Structure Commands

Warning: Chimera2 is not yet released and the command syntax below is subject to change.

Chimera2 is currently mostly controlled by typed commands. We do not yet have much user documentation for the commands although many are the same or similar to Chimera 1. There is Python programming documentation for the commands which reveals all available options.

open 2bbv color #1 bychain style stick /b Mouse drag to move.
File is fetched from PDB in mmCIF format and cached in ~/Downloads/Chimera/PDB Each chain gets its own color. Change chain b to stick style. Rotate by dragging mouse, translate by dragging mouse with option key pressed.

~display /c ribbon /c Mouse click to select an atom. Press up-arrow key.
Hide chain c atoms. Display backbone ribbon Click to select showing green outline, shift-click to add to selection, click background to clear selection. Up arrow and down arrow keys expand and unexpand selection.

color sel gold surface #1 ~display
display :HOH
style sphere
Use "sel" to refer to selected atoms in any command. Solvent excluded surface for each chain. Show waters as red spheres.

sym #1 sym #1 assembly 1 view
Assemblies for 2bbv
1 = complete icosahedral assembly (60 copies)
2 = icosahedral asymmetric unit (1 copies)
3 = icosahedral pentamer (5 copies)
4 = icosahedral 23 hexamer (6 copies)
PAU = icosahedral asymmetric unit, std point frame (1 copies)
XAU = crystal asymmetric unit, crystal frame (5 copies)
List mmCIF assemblies. Show the assembly named "1". Bring all models into view.

light full sym #1 assem 3
set bg white
set silhouette true
sym #1 clear
~display
ribbon
save ~/Desktop/2bbv.png
display
~ribbon
light flat
Show direct and ambient shadows. Show pentamer assembly, set background color to white, show thin black edges. Show asymmetric unit as ribbon and save image. Flat lighting with silhouette edges.

buriedarea /a with /b

sasa #1 & ~:HOH
contacts #1 movie record super 3 ; turn y 3 120 ; wait ; movie encode ~/Desktop/spin.mp4 quality high
Buried area between /a and /b = 1900.4
area /a = 15385, area /b = 14989, area both = 26573

Solvent accessible area for #1 & ~:HOH = 34093
8 buried areas:
  B A 1900, C A 1865, C B 1836, C F 766,
  A D 738, B E 709, C N 211, N F 93
Compute solvent accessible buried surface area between chains A and B. Also compute total solvent accessible area excluding waters. Display contact graph between all chains. Record movie spinning 3 degrees for 120 steps. Commands are on one line.

Example Density Map Commands

open emdb:1080 volume #1 level 0.9 Click contour level mouse mode then drag with right mouse button. vol #1 enclose 1e6 step 1 color tan
Open EM Databank map 1080. Hover mouse over map reports contour level 1.675 in status line. Then change level. With Mac one-button mouse drag while pressing Command key. Set level to enclose 1,000,000 cubic Angstroms, show full resolution and set color.

light full
set bg gray
set silhouette true
open 1grl Click move selection mouse. Click atom to select. Then right-mouse drag to move molecule into map. fit #2 in #1
volume #1 transparency 0.5
color bychain
Lighting with shadows, plus thin black edges. Open atomic model to fit in map. Can also use rotate selection mouse mode. Locally optimize fit of atomic model in map. Make map 50% transparent.

molmap #2 10
vol #3 style mesh
vop subtract #1,3 minRMS true
vol #4 color pink transparency 0
~display ; ribbon
close
open emdb:1273
volume #1 region all showOutline true
Create simulated map for atomic model at 10 Angstroms resolution and show as mesh. Subtract simulated map from experimental map. Open tomogram of a T-cell, single-plane grayscale displayed because of large map size. Show all planes of tomogram, grayscale rendering.

open eds:1a0m open 1a0m
style stick
vol #1 level 1.0 style mesh
vop zone #1 atoms #2 radius 2
vol #3 level .5 style mesh transp 0.6
Open x-ray map for PDB 1a0m from Uppsala Electron Density Server. Show atomic model and x-ray map as mesh. Show map zone within 2 Angstroms of atoms.