List of Chimera features suppported by the Collaboratory (as of 1/03)
------------------------------------------------------------------------

Below is a list of all of the features in Chimera that are accessible via
the menus or through the command line interface.
The status for each feature can be any of the following:

"works"        - the results of issuing a command or interacting with a menu or panel _are_ propagated
                 to the remote end. 
                 N.B. Some Chimera features are controlled through a graphical interface (e.g. Pseudobond Panel).
                 For these features, I have specified whether or not the state of the interface components
                 (colors, settings) are propogated to the other side (i.e. if you color a molecule blue through
                 one of several graphical user interfaces, both the molecule and the interface that controls
                 model color should have the same color on the remote end)                  


"doesn't work" - the results of issuing a command or interacting with a menu or panel _are_not_ propagated
		 to the remote end

"N/A"          - the above scenarios are not applicable to this command or panel interaction
                 (i.e. it does not make sense for this feature to work over the Collaboratory)


Basic PDB/VRML/Mol2 model support
========================================================================

Models opening works (verified)
Model manipulation by the standard mouse controls works (verified)
Model closing works (verified)

NOTE:
As of this release, the collaboratory supports the following types of models:
  -PDB  [.pdb, .ent]
  -Mol2 [.mol2]
  -VRML [.vrml, .wrl]

  The collaboratory will not behave correctly when dealing with other types
  of models.
========================================================================





Menus
========================================================================

File menu
	Open            - works 
	Open Session    - doesn't work 
	Save Session    - N/A
	Save Session As - N/A
	Close Session   - works
	Save Image      - N/A
	Quit            - N/A
      
Select menu
	Amino Acid Category   - works
	Chemistry	      - works
	Draw Mode 	      - works
	Structure	      - works
	Clear Selection       - works
	Midas Atom Specified  - works
	Sequence              - works 
	Zone	              - works
	Selection Mode        - works
	Select All            - works
	Save Selection        - works
	Saved Selections      - works
	Construct Selector    - works


Actions
	Color       - works
	Label  	    - works 
	Focus       - works
	Atoms/Bonds - works
	Ribbon      - works
	Surface     - works
	Target      - works
	Inspect     - works
	       
Tools
	Collaboratory   - N/A (Hmmmmmm)
	DelPhi          - doesn't work
	Docking         - doesn't work
	Ensemble        - doesn't work
	Homology
	   AlignPlot        - doesn't work
	   KeepSticks       - doesn't work
  	   MPOSE            - doesn't work
   	   MSF Viewer       - doesn't work
	   Minrms Plot      - works
	   Multalign Viewer - doesn't work
	Inspectors
	   2D Texture       - works
	   Adjust Torsions  - doesn't work
 	   Angles/Torsions  - doesn't work
  	   Color Editor     - N/A
	   Distances        - works (+most GUI elements replicated)
 	   Lens Inspector   - works (+most GUI elements replicated)
           Model Panel      - works (+most GUI elements replicated)
           PseudoBond Panel - works (+most GUI elements replicated)
           Selection Inspector - works (-label color, +most GUI elements)
	Keyboard            - N/A
	Molecular Dynamics  - doesn't work
	Programming         - N/A
	Utilities
           AddH                 - works
	   Benchmark            - N/A
	   FindHBond            - works
	   MainChain            - works
	   Model Panel          - works (+most GUI elements replicated)
	   PBReader             - N/A
	   PipesAndPlanks       - works
	   Reply Log            - N/A
	   ResProp              - works (-GUI elements replicated)
	   Ribbon               - works
	   Ribbon Style Editor  - doesn't work
	   Scale Bar            - doesn't work
	   Simple Session       - N/A
	   Structure Mmts.      - works
	Viewing Parameters
 	   Camera     - works            
	   Effects    - works
	   Rotation   - works
	   SideView   - works
	Volumes   - doesn't work
		
========================================================================




Command-line commands
========================================================================

ac        - N/A
alias     - N/A (created alias cannot be used on remote end)
align	  - does not work
angle     - N/A (only reports on local end)
brotation - doesn't work
cd        - N/A (won't change directory on remote end)
center    - works
chain     - works
clip      - works
close     - works
cofr      - works
color	  - works
colordef  - N/A (color definition not valid on remote end)
conic	  - doesn't work
copy	  - N/A
display	  - works
distance  - works
echo	  - doesn't work
freeze	  - works
getcrd	  - doesn't work (only reports on local end)
help	  - N/A
ksdssp	  - N/A
label	  - works
labelopt  - doesn't work (??)
linewidth - works
load	  - doesn's work (??)
longbond  - works
match	  - works
matrixcopy- works
modelcolor- works
modeldisplay - works
move      - works
msms	  - works
neon	  - doesn't work (wont display image on remote end)
objdisplay - works
open	  - works
pdbrun	  - doesn't work (won't execute on remote end)
push/pop  - works (can only pop on side that was pushed)
rainbow   - works
read	  - works
represent - works
rescolor  - works
reset	  - works (can only reset on side that it was 'savepos'ed)
ribbon	  - works
ribbonjr  - doesn't work
ribrepr   - works
rock	  - works 
roll	  - works 
   (n.b. for 'rock' and 'roll' commands, only user who initiated motion can 'freeze' it)
rotation  - doesn't work
save	  - N/A
savepos   - N/A (can only recall pos on side it was saved)
scale	  - works
section   - works
select    - works
set/unset - N/A
show      - works
sleep     - works
source    - works
stop      - N/A
surface   - works
surfcat/surfrepr - ???
surfcolor - works
swapaa    - ???
swapna    - ???
system    - N/A (will only send command to local system)
tcolor    - ???
texture   - ???
thickness - works
turn      - works
vdw  	  - works
vdwdefine - works
vdwdensity- works
version   - N/A
wait      - works
window    - works
write     - N/A (will only write file on local side)

========================================================================




COLLABORATORY FEATURES
========================================================================

**Conduct real-time shared modelling sessions among multiple participants
**Supports all Chimera core features
**Remote pointer mechanism
**Join session that is already in progress

Hub Features:
**Session administration capabilities
========================================================================



KNOWN BUGS
========================================================================

**Modifying the color of the same object (i.e. pseudobond) simultaneously on both
  sides of the Collaboratory can result in an error. 
  This is due partly to the way chimera handles colors in the color panel

**Opening models at the same time on different nodes can result in multiple 
  models being opened with the same id. 

**Chaining a model, then selecting one of the pseudobonds will cause an error 
  (not fatal, though)

**HighlightLens properties are not propagated to a user who enters an in-progress
  Collaboratory session
========================================================================