New Density Tools feedbacks

Case number:845813-2012071
Topic:Game: Tools
Opened by:Nicm25
Opened on:Friday, September 17, 2021 - 21:22
Last modified:Saturday, September 18, 2021 - 15:10

It may be consolidated into this thread for while while new ED tools are released frequently.
I hoping this will be place for little developer advice.

first suggestion:
in 2021-09-18 devprev relesed tools...
"Select Cloud"
I think they take it to mean "choose the clouds."
maybe "Select at Density" would be better.
and sorry, I'm not native English speaker, but can this suggestion help?

(Fri, 09/17/2021 - 21:22  |  2 comments)

Nicm25's picture
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also ED tools that players needed in past....

add variety of coloring and shapes for notes.

Evolve the 'Center Protein on Density'.

additional Lua commands.

most of the other feedback was about trimming the density display and editing voxels.
and things that change and affect Rosetta functions, such as special bands.
if you have any suggestions that we haven't figured out yet, we can link to them following reply to this. ;D

Susume's picture
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What the Select Cloud tool does (correct me if I'm wrong):
* selects a set of residues (amino acids), using selection interface

Some things it does not do:
* select part of the cloud
* improve the fit of your protein in the cloud
* notice how well your protein fits in the cloud
* move the cloud
* move the protein
* give you information about the cloud, or about your protein

What it uses to choose the residues:
* Radius setting on the ED panel
(if the radius is 100%, Select Cloud will select all residues, regardless if they are in the cloud)
* Camera position
(because the visible sphere when radius is < 100% is defined by center screen)

Some things it does not use to choose residues:
* zoom, zoom-and-trim (shift-Q)
* ED threshhold
* ED 'Trim Density' setting
* field-of-view trims, such as ctrl-shift-drag or ctrl-alt-drag
* how well your protein fits in the cloud

In the sci chat, there was a bit of confusion when the devs would say 'move the cloud.' I think most players think of the cloud as locked in space, so they can only move their protein relative to the cloud and not vice versa. The devs may have meant 'move the field of view.' If your ED radius is set to <100%, moving the camera has the effect of displaying a different subset of the cloud. The cloud has not moved, but you are now looking at a different bit of it. The sphere of cloud displayed is generally centered on center screen (although by zooming out you can sometimes move off center and still see the sphere). Since it is tied to the Radius setting, and does not act on the cloud, a better name for the tool might be 'Select by Radius.'

The phrase 'Within the Electron Density cloud' in the tooltip is kinda confusing. Many players think of the entire cloud as existing even when only a portion is displayed. A protein segment that was 'in' the density a moment ago is still in it (assuming the protein has not been moved), even if you can't see it right now. A protein segment can be within the overall outline of the cloud but still be 'outside' the cloud if there is a hole in the density. Placing every segment 'in the cloud' (in the strict sense of not overlapping a density hole) is a very specific player goal that directly affects the score. Sometimes we say 'in the cloud' to mean 'roughly located within the cloud outlines,' but sometimes we mean 'completely covered by density, not in a density hole'. A tooltip that uses this phrase might mean either (and in this case does not mean the one that gets winning points).


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons