New ED thoughts and bugs

Case number:699969-995591
Topic:General
Opened by:AsDawnBreaks
Status:Closed
Type:Bug
Opened on:Friday, July 19, 2013 - 14:18
Last modified:Sunday, August 18, 2013 - 21:39

1) When I click align to density, it aligns, then reverts. It is now useless.

2) Trim density is too touchy. Moving the slider a little bit reduces the cloud too much for me.

3) I would like to be able to preview my density trim like we do with threshold, so I'm not blindly guessing and have to go back and fix numerous times.

(Fri, 07/19/2013 - 14:18  |  17 comments)


bertro's picture
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on 2): also return the current value of trim when reopening the Trim Density window. Currently it only defaults to far each time.

And make it (or add) a numerical input box like the CI one. Much more precise and easy to control.

bertro's picture
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Bug: When ED is set to "None" and you press tab in an empty space "that is still a valid density spot" (but of course invisible since density is set to None) a Note/Purple dot is still created.

This happens even outside of the visible Trim area as long as it is a "valid density spot". I believe not Purple Dots should be "created" on invisible density spot. It is ok to keep pre-existing Purple Dots.

Susume's picture
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When you have trimmed the density and try to add a purple dot, the dot adheres to the non-visible density in the foreground instead of the further-in density you can see and point to. It is rather startling if you are zoomed in and the dot appears suddenly as big as your face.

Joined: 09/21/2011

yep, trim makes placing dots tricky. placing dot on "visible" location would be ideal. if this isn't possible, a "preview" trim slider would make it slightly less tricky.

brow42's picture
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Focus on Density also centers on the full density, not the visible part, which is kinda non-intuitive.

bertro's picture
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Suggestion:

When trying to visualize the protein in the cloud, I would like to be able to have ONLY some of the sidechains showing (to declutter the view a bit).

That would mean I would perhaps select some segments and click "Show only selected sidechains" in View or something similar.

brow42's picture
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I've wanted this too. Work around tip: Banded sidechains are always visible.

bertro's picture
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Right but the bands don't follow well if you move, they stretch and make a mess of the view. Not helping.

katfish's picture
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Wanted to jump in here and let you know that we've got this bug on our plate. Working on getting it resolved. Thanks for the heads up!

Joined: 09/21/2011

i assume, you mean that placing the dots is on your plate.
please also note that the original suggestion is a slider similar to the threshold preview slider which would be a super cool tool. thanks

katfish's picture
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Noted, thanks kars.

Susume's picture
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Can we please have the purple dots persist through track changes, saves and loads? It is maddening to have them all disappear.

beta_helix's picture
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Topic: Developer Preview » General
Type: DevPrev Issue » Bug

karstenw & Susume, you bring up a good point about the many different ED bugs in this thread.

I fear that the many different important ED issues that have been brought up in this feedback might get lost, or if the original one gets resolved it will be difficult to mark this feedback as Closed.

If someone can create a specific feedback for each issue (with a clear title describing each problem), then it will be easier to address each of these one at a time.
(AsDawnBreaks, maybe you would be willing to do this, since you started this useful thread?)

I really just don't want any of these issues (such as the last one that you just pointed out, Susume) falling through the cracks!

Thank you!

Joined: 04/15/2012
Groups: Beta Folders

Can do!

Joined: 04/15/2012
Groups: Beta Folders

Did I set them up OK?

beta_helix's picture
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perfect, thanks!

Joined: 04/15/2012
Groups: Beta Folders
Status: Open » Closed

Split.

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