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 |