What happened to Hydrophobic view mode?

Case number:671071-730401
Topic:Game: Other
Opened by:xiando
Status:Closed
Type:Bug
Opened on:Thursday, December 18, 2008 - 03:51
Last modified:Tuesday, January 13, 2009 - 22:19

Until this last update hydrophobic view mode was a available by pressing ctrl-shift-H, then ctrl-shift-s to return to score mode.

I used this mode extensively to assist in side chain tweaking. It has now been either disabled by removing the hotkey link or removed entirely from the game.

Can you please re-enable? I am functionally crippled without it
as I use side chain tweaking extensively.

Not asking for a new feature, just allowing me to use a feature that was deleted for imo no good reason

(Thu, 12/18/2008 - 03:51  |  7 comments)


axcho's picture
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I'll ask about it. I don't think any features were purposefully removed, so hopefully it's just a simple mistake.

xiando's picture
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Yes. I expected as much, but between that loss and the unstable shake output, I'm kinda floundering. Still able to score, but not in the manner I'm used to performing for the project.

My guess is the hotkey link was deleted or commented out. FWIW, this is a very useful view mode, for instance when doing fine tuning on the protein as was taught in many of the constrained puzzles leading up to CASP.

And while I can't demand anything, I urge you guys to re-enable hydrophobic view mode

regards,

Let me try again. You removed a function that was useful in order to please another player by changing the hotkeys.. Please re-enable it immediately

xiando's picture
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Ok, downloaded the latest update. Although I have no idea what was fixed (presuming this was a bug-fix release), and I'm wondering how difficult it is to renable a hotkey. Who asked to have this removed in the first place? The "competition"? Sorry, but I've been very patient til now and am getting a little impatient at watching others bugs be fixed and mine ignored. This was a trivial fix and could have been applied without even the need for thought. just re enable the hotkey or re install the removed code...

I don't understand the "Ask about it" in your reply? Just tell Seth that this is the view mode that he promised to re-instill in the View menu and never did, leaving it as a "hidden" view mode for the last 5 months. That ought to clarify which view mode I'm talking about.

Or am I to understand that banding and isolated wiggles are the new paradigm for foldit?

I do see that someone spent time creating those two new "hidden" view modes. This is a bug, not a feature request.

admin's picture
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Status: Open » Closed

The Hydrophobic view as such has been removed. The colours shown in Hydrophobic mode are now part of the default colouration. What we do intend for the future is more configurability of the colours used in general; so you could assign polarity-colouring to sidechains but energy-colouring to the backbone, all in the same view.

In view of this, I'm closing this topic.

xiando's picture
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Part of the point to hydrophobic mode was that it had no coloration, aside from the blue and orange side chains, so was less distracting than coloration mode. It also showed clashes in a different way that the score view mode does, which is beneficial when moving side chains.

Due to the removal of realtime coloration calculations and wavy animation during wiggle, it was also measurably faster

axcho's picture
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I'm thinking that we'll eventually add support for custom color schemes (that could be switched easily), which could help. I think that's what admin was saying. Would you like to suggest options and elements that should be included in such a feature?

xiando's picture
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Axcho,

Please open the last version prior to the "major" issued update around Thanksgiving break.

Open a competition puzzle

Press shift-ctrl-H to enter hydrophobic mode
Note the colors of the side chains and backbone, but pay special attention to the color of the backbone

In the View menu, enable the following (disable all others): "clashes", "glow", "relative score coloring", and "show all side chains(slow)".

Manually rotate a side chain to cause a minor clash. note change in coloration and "glow of affected areas.

Manually rotate a side chain to cause a major clash. Note change in coloration and "glow" of affected areas.

If they exist, note bright green glow areas.

The color scheme I'm talking about is the one that is designed for Hydrophobic mode.

Note also, that while wiggling, the standard shimmering water animation seems to be suspended.

The specific color scheme and associated effects should all be in the code specified in the first step.

If necessary, I will open the old version and send screen shots.

thank you

PS> I will submit some snapshots of ideas shortly

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