List of Chimera features suppported by the Collaboratory (as of 1/03)
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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
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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.
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Menus
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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
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Command-line commands
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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)
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COLLABORATORY FEATURES
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**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
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KNOWN BUGS
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**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
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