Manual

Monolith is manipulated via the chat window of channel 2 (currently)

Most commands follow a simple syntax of "command <value> / selection"

Selections can be specified as followed:

@ - specifies a atom name
: - specifes a residue number or name
zr<value - specifies all residues within a "value" distance of primary selection
za<value - specifies all atoms within a "value" distance of primary selection.

color <1,0,0> / @??',??'',P,OP?

This command will color all atoms that have 2 character names and that end in a one or two single quotes, or  is a phosphor, or who's name starts with OP (such as OP1 and OP2).  This command is useful in selecting the backbone of a DNA structure.

color <0,1,0> / :20-173

This command will color all atoms in all residues who are numbered from 20-173.


 

Command Summary

 Implemented Command
 Description
    color <R,G,B> / selection  color selection by a specified RGB vector.  For example, "color <0,0,1>" would color all atoms blue.
   alpha <value> / selection
 change alpha (transparency) of atom selction.  <value> ranges from 0 to 1.  0.5 would be half transparent.
   text <value> / selection
 assign additional text to floating label.  "text" command by itself deletes any specified text on selection.
   monitor / selection
 turns floating label over selection and will alos include any text specified by the "text" command.
   open <url/accession ID>  Load accession ID from Rutger's Protein Databank.  Alternate http(s) URLs will be supported shortly. *** note - region limited to 15,000 prims, so, and structure with a number of atoms (spacefilled) greater than the remaining prims in the region (max 15,000), will have issues rezzing
   die / selection
 Causes selection to self-delete and be de-rezz'd from viewing
   glow <value> / selection
 Sets selection to glow by value (0.0-1.0).  Helps with highlighting.
   phantom / selection
 Sets selection to phantom.  Allows other other objects or avatars to pass through.
   nonphantom / selection
 Sets selection to non-phantom. Selection becomes "solid" and collisions will be detected.
   physical / selection
 Set selection to physical and caused selection to be affected by Second Life physics engine.  Not too useful for molecular visualization, but fun to watch. :-)
   nonphysical / selection  Sets selection to nonphysical. Atoms will not return to former position, but will stop rolling away.
   reset / selection  Sets selection to return to locations specified by original structural data.
   atomscale <value> / selection  Changes atom selection scale value by <value> multiplier.
   shiny0 / selection  turns off shininess of atom selection
   shiny1 / selection  sets atom selection to low shine
   shiny2 / selection
 sets atom selection to medium shine
   shiny3 / selection
 sets atom selection to high shine
   insert / selection
 renders atom selection inert.  No further structural visualizations can be done.  Useful for packaging a canned session and giving it to others.  Structure elements are not linked.
New - 2/4/2009
  molscale <value>  Scales over-all structure to specified value.  Current structures are rezz'd at scale of 1A = 1 meter.  Thus, they are relatively huge at the moment.
     
     Commands being implemented but not available yet
   close  close current structure (die command does the same thing but is not quite intuitive.
   ballandstick / selection
 Sets atom selection to be displayed as ball and stick
   spacefilled / selection
 Sets atom selection to be display as space-filled model (no bonds present).  This is the current display mode now.
   save <session>  Will save current session as specified name.
   load <session>
 Re-loads prior session and restores last know color/effect/text scheme.
   move <x,y,z>
 Move structure to x,y,z coordinate.
   distance atom1 atom2
 displays distance measurement between two atoms