Actions:

Actions are commands that tell spock to do something--that is they are commands that are executed, as opposed to selections, which limit an action to a specified group of atoms or vertices.

Note: SEL following a command indicates that the command may by followed by an object selection string, N represents a number, L represents a single letter for a chain name. Bracketed items separated by a vertical bar indicate that one of the options may be used.

For the coloring commands the options mean: X a color number, d the default color, u undo the last color change, n color by object number. The i option, only available for bonds, means to ``invert'' the color to display the bond in the secondary style.

• Output/Listing
  • ls/list [,SEL] (list atoms)
  • blist [,SEL] (bond list)
  • hblist [,SEL] (h-bond list)
  • mlist (list molecules)
  • modellist (list models)
  • slist (list sheets)
  • hlist (list helices)
  • tlist (list turns)
  • rlist (list residues)
  • ilist (list interaction)
  • mass [,SEL] (calculate mass)
  • help list (get help on list format)
  • show helices: get information on helices
  • show sheets: get information on sheets
  • show rotation: print rotation matrix
  • show variables: prints all ``SP'' environment variables
  • show version: prints the version number
• File
  • read=file.ext (read a file)
  • read -s=file.ext (silently read a file)
  • fetch=pdbid.pdb (check in the PDB directory for file. If not found, fetch it from the pdb's ftp site)
• History
  • pause, resume, abort
• Set/Counting
  • set center [,SEL] (set center of rotation)
  • set centre [,SEL] (set centre of rotation, for the Brits)
  • set list format
  • set list command
  • set radius=X [,SEL]
  • set structure=<H|S|C|T> [,SEL]
  • set chain=L [,SEL] (sets chain name to ``a'')
  • set distance=X [,SEL]
  • set vdistance=X [,SEL] (vertex distance)
  • set dp=X [,SEL] (distance partner)
  • set charge=X [,SEL]
  • set p=X [,SEL] (potential)
  • set ap1=X [,SEL]
  • set ap2=X [,SEL] (atom properties 1 and 2)
  • set sa=X [,SEL] (surface area)
  • set it=N [,SEL] (interaction type)
  • set iv=N [,SEL] (interaction value)
  • set $a=value (define environment variable)
  • count $a=SEL (define environment variable as the number of atoms in the selected set)
• Viewing
  • center (recenter the view)
  • centre (recentre the view, for the Brits)
  • view=X (set/save view number)
  • xr/yr/zr=X (rotate about axis X degrees)
  • Xt/Yt/Zt=X (translate X Ångstroms)
  • xt/yt/zt=X (translate in fractional screen coordinates)
  • zoom[=X] (print magnification, or set it to X)
  • look[=radius][,SEL] center on the selection, only color those bonds within the radius of the center of the selection.
• Coloring
  • bc=<X|d|d2|u|i> [,SEL] (bond)
  • ac=<X|d|d2|u> [,SEL] (atom)
  • wc=<X|d|u|n|s> [,SEL] (worm)
  • hc=<X|d|u|n> [,SEL] (helix)
  • sc=<X|d|u|n> [,SEL] (sheet)
  • nc=<X|d|u|n> [,SEL] (note/annotation)
  • ic=<X|d|n> [,SEL] (interaction)
  • lc=<X|d|u|n> [,SEL] (label)
  • vc=<X|d|u|a|n> [,SEL] (vertex/surface)
  • cc=X (cap color for clipped surfaces)
  • bgc=X (background)
  • hbc=X (H-bond)
  • cac=<X|n|a[tom]|b[ond]> (CA trace)
  • ilc=X (interaction label)
• Control commands
  • quit
  • QUIT (unconditional)
  • delete [,SEL] (deletes selected atoms)
  • zap (delete all)
  • mutate=AA [,SEL] (mutates selection to aa)
  • mac=NAME (call macro)
  • macdef=NAME (define macro)
  • endmac (end macro definition)
  • contour2d=X/contour3d=X (make 2D/3D contour)
  • label=STRING [,SEL] (make custom label for first atom in selection)
  • subdef=NAME [,SEL] (define an atom subset)
  • vsubdef=NAME [,SEL] (define a vertex subset)
  • draw=<on|off> (toggle graphics display)
  • remake (rebuild all objects from their definitions)
  • connect (recalculate bonding)
  • structure (calculate secondary structure)
  • renumber=N [,SEL] (renumber the selected residues sequentially, starting at N)
• Command-line calculator (examples)
  • #1+1 (calculate single value)
  • #i=1 (define variable)
  • #f(x)=ap1(x) (define function)
  • #d()=ap1()+ap2() (apply function to property for all atoms)
  • #show variables (list variables)
  • #show functions (list functions)
  • #show angles (trig function angle setting)
  • #set angles <degrees|radians> (tell trig functions to use radians or degrees)