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.
|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