Maps
| 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"
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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
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Molecules
| 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"
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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"
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