Chimera Quick Reference for HIV and ParM Tutorials

HIV and ParM tutorial notes. Chimera web site and download, Documentation: volume data guide and tools and commands


Volume dialog Tools / Volume Data / Volume Viewer
Fitting dialog Tools / Volume Data / Fit in Map
Fit only selected atoms fit dialog, fit "selected atoms", option "Move whole molecules" false
Correlation value Fit dialog, Options "use simulated map"
Simulated map calculation "molmap #3,4 17"
Freeze map motion Active models checkbuttons beneath command-line.
Or "activate all" and "activate only" buttons in Model Panel.
Determine map symmetry axis volume dialog File / Duplicate, rotate map copy, fit,
axis reported in reply log
Color surface select surface with ctrl-click, the Actions / Color / blue
Transparent surface click color button, adjust opacity slider
Fade surface "surftransparency 100 #0 25"
Single transparent layer volume dialog, Features / Surface and Mesh Options, one transparent layer
Color map to match atoms Tools / Volume Data / Color Zone
Volume outline box volume dialog, Features / Data Display Options,
or command "volume #0 showoutline true"
Morph between maps Tools / Volume Data / Morph Map, or command "vop morph #0,1"
Map grid change "vop resample #2 ongrid #0"
Save map volume dialog, File / Save Map As...
Difference map "vop subtract #2 #5 minRMS true"
Flip handedness of map "vop zflip #2"

Visualization Environment

Command-line Favorites / Command-line
Text results Favorites / Reply Log
Command help "help sym"
Center and zoom Actions / Focus
Move in/out of screen ctrl key + middle mouse button
Save image File / Save Image
Background color "set bg_color white"
Silhouette edges Tools / Viewing Controls / Effects, silhouettes.
High quality lighting Tools / Viewing Controls / Lighting, quality "glossy"
Raytraced image (shadows) File / Save Image, Raytrace with POV-Ray -> true
Record movie "movie record", ...,
"movie encode output ~/Desktop/movie.avi"
Pause before executing
next command
"wait 50"
Toolbar buttons Favorites / Preferences, category Tools,
check "On Toolbar" buttons


Color PDB chains command "rainbow chain"
Display atoms Actions / Atoms / show.
Select waters Select / Residue / HOH
Delete atoms Actions / Atoms / delete
Select one chain Select / Chain / G
Select specific residues "select #1:163-307", "select :33,34,36,40"
Invert selection Select / Invert, or right-arrow keyboard key
Hide ribbon Actions / Ribbon / hide
Red-to-blue color one chain command "rainbow"
Measure rotation command "measure rotation #1 #3 showslab true"
Align molecular models Tools / Structure Comparison / Match Maker
Symmetric molecule copies "sym #1 group c3 coordinateSystem #0
center 205,205,205"
Ellipsoid representation of molecule "measure inertia #1:.G"
Move only selected atoms Tools / Movement / Movement Mouse Mode,
move selection
Calculate domain rotation angle "match move false showmatrix true
#1:163-307 #7:163-307"
Align molecules with identical sequences "match #1:1-162 #7:1-162"
Morph molecules Tools / Structure Comparison / Morph Conformations, command "coordset #4 1,41"
Show only backbone atoms Actions / Atoms / backbone only
Show bond length mouse over bond to see popup balloon
Energy minimization Tools / Structure Editing / Minimize Structure
Helix molecule copies "sym #3 group h,1,-24.3,-165.4,6 coord #2"
Color multiple molecules "rainbow models #3,4,5"
Steric clashes "findclash #4.2 intersubmodel true select true"

Maps or Molecules

Model Panel Favorites / Model Panel
Hide map or molecule Favorites / Model Panel,
checkbuttons in s (shown) column
Rotate by specified angle "turn z 120 center 207.9,204.9,0 coord #0"
Shift my specified vector "move 207.9,204.9,0 model #0 coord #0"
Fly movie motion "savepos bound", "savepos far", "reset bound 50".
Undisplay map or molecule "~modeldisplay #0", "modeldisp #2"
Align coordinate axes "matrixcopy #1 #7"