View Options: Colours for component scores

Case number:845833-987694
Topic:Game: Display
Opened by:keypad5
Status:Open
Type:Suggestion
Opened on:Saturday, May 8, 2010 - 04:27
Last modified:Saturday, May 16, 2015 - 18:43

I think it'd be helpful to be able to see the component scores (backbone, sidechain, clashing etc.) displayed in colour the same way that segment scores can be displayed in colour (i.e. with the relative score colouring turned on).

Two ways to go about this could be to;
a) have the entire segment (backbone and sidechain) coloured in accordance with a user selected component score (e.g. clashing or backbone).
b) have the sidechain coloured in accordance with its score, and the backbone coloured in accordance with its score. This option would only work for the sidechain and backbone components, and may result in a very colourful protein, but I think it could be quite useful.

After bringing this up in chat there was some discussion about how this would work for colourblind folders. Having mused on it a little more, I think that since these suggested settings aren't calling for the introduction of any new colours then I believe they will work just as well in the colourblind mode. (But not being colourblind I can't really know this for sure! :-P)

How would this help the folding process?

Here's a bit of information that outlines the genesis of this suggestion and why I'd find such a colour option to be useful:

Lately I've been approaching folding a little differently. Firstly, I usually fold with "relative score coloring" turned on and "show bondable atoms" turned on too, but have only recently started to use the "Color: Score" setting instead of the default "Color:Score/Hydro" setting. (I've been using the "Color: Score" setting because I'm now familiar enough with the proteins to recognise the hydros based on shape and bonding and don't need the orange and blue colours to distinguish phobics from philics). And once I started viewing the hydros outside of their defaul blue and orange colouring it got me thinking about how else they could be coloured.

Secondly, I've been using scripts to help identify low component/part scores (thanks aap!) (e.g. low backbone scores, low sidechain scores etc.) The problem with using the scripts is that they simply give you back a list of numbers that identify low component scores, and then you have to hunt through the protein to find those segments and get to work on them. And I've actually made another script to help me find segments within the protein. So there is a lot of scripting and number checking to find the areas that I want to work on.

Having a viewing option that would allow me to instantly recognise where these low component scores are would make the areas I want to work on a lot more immediately accessible.

Any thoughts?

(Sat, 05/08/2010 - 04:27  |  6 comments)


Joined: 04/19/2008
Groups: None

This could be helpful indeed. Areas that only have a negative clashing score are often easily repaired by wiggling. Areas that have a low backbone score, however, often do not benefit from wiggling and have to be rebuilt completely.
After threading from an alignment, one could see which parts of the protein need to be rebuilt (by changing the coloring to backbone score only) and which parts will benefit from a later wiggle (changing the coloring to clashing score).

Joined: 09/18/2009
Groups: SETI.Germany

I second that.

spmm's picture
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Joined: 08/05/2010
Groups: Void Crushers
Status: Open » Closed

Timo has written a script for this now closed

jeff101's picture
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Joined: 04/20/2012
Groups: Go Science

Which script does this?

jeff101's picture
User offline. Last seen 22 hours 40 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Status: Closed » Open

I like the idea of letting the player choose which score or subscore
to use when coloring each amino acid in the protein. If this idea
were implemented, it would also help to do the following:

(1) List in the "View" menu what score/subscore is being used at present
for coloring.

(2) In the "Segment Information" box brought up by Tabbing on a residue,
somehow designate which score/subscore is being used; for example, list
the score or subscore's name in all-caps, or put a string like "*" or
"sets color scheme" to the right of it.

jeff101's picture
User offline. Last seen 22 hours 40 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

If you are already coloring by score,
it would be nice to not have to enter the View menu
to change which score/subscore you are coloring by.

Perhaps if a "Segment Information" box is open,
you could click on it and then use keys like
PageUp, PageDown, the up and down arrows, or Return/Enter
to change which score/subscore you are coloring by.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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