Contact Map Tool

Case number:699969-998081
Topic:General
Opened by:karstenw
Status:Open
Type:Suggestion
Opened on:Friday, June 27, 2014 - 13:05
Last modified:Tuesday, July 15, 2014 - 11:00

I'd like to "select all" contacts and have at least the contacts with the highest degree of certainty show on my protein. Doing this by hand is way slow and time is tight during CASP.
Maybe also a "select all empty" contacts too. This tool would allow all contacts with red lines only to be selected. These 2 "select all" options would be extremely handy.
I would also like to click on a red or green contact line in my puzzle and make it disappear like we can do with bands.
If any one reading this can make a script that uses weak bands to substitute for "select all" until these tools are made, that'd be awesome.

(Fri, 06/27/2014 - 13:05  |  13 comments)


Joined: 09/24/2012
Groups: Go Science

This script partly answer your request:

Contact Cement 2.02

In the current version, the intention was to (not sure all of this is implemented yet in the public version - still working on it):
1-Checks for contacts with non-zero heat.
2-Displays some statistics (number, mean heat, median heat) about any such contacts found.
3-Bands any contacts above a user-specifed heat cutoff.
4-Weights the band strength in function of heat, from 0.5 to a user-defined max heat
(strength set to low value helps for a better informative display, big values could be good for further work, but it gives something less readable on screen when there are many bands)
5-Allow you to select a limited number of bands in case there are too many contacts

I use it to put bands, then I can enable or disable the bands manually or with scripts.
To Do: If I or anybody finds time, we could additionally implement your ideas:
-make it work better (not sure it's bug free)
-function 5: I've to find a solution for a kind of intelligent select (random or following some criteria)
-function 5: it would be great to be able to delete redundant bands (for example keep only bands from starts and end of 2 sheets, delete bands inside a helix etc)
-select all empty contacts: great idea !
-click on red/green contact? impossible via script, this is for dev
but, once the contacts are banded, you can delete the related bands (not the lines)

Note that the script does not select anything on the contact map: red or green lines do not appear on the screen (only bands): this is for dev

Joined: 09/21/2011

thanks bruno

spmm's picture
User offline. Last seen 40 weeks 4 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers

Yes please - a button to select and show any green square would be a real time saver - particularly as we need to reset the contact visualisation every time we open the puzzle or change tracks.
I usually put my own bands on but repeatedly clicking the green squares is time consuming and probably damaging to my eyes.

alcor29's picture
User offline. Last seen 1 day 13 hours ago. Offline
Joined: 11/16/2012
Joined: 09/24/2012
Groups: Go Science

also see

http://fold.it/portal/node/997925

It would also be nice to be able to select a number of points like with the mouse in windows (click and hold). This would save time and nerves (not being obliged to click precisely point by point).

jeff101's picture
User offline. Last seen 19 hours 34 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

Please see http://fold.it/portal/node/997613 as well.

Joined: 11/10/2007
Groups: Window Group

Would you prefer "select all" and "select all empty" maintain any existing selection and add to it, or first clear any existing selection?

spmm's picture
User offline. Last seen 40 weeks 4 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers

Thanks Seth, I guess if you have things selected already then best to just add the select all (green ones)as it is easy to clear all selected already.
Is 'select all empty' selecting the non-green squares? or the green squares which don't have contacts showing? I don't get this one sorry can't answer.

alcor29's picture
User offline. Last seen 1 day 13 hours ago. Offline
Joined: 11/16/2012

I should think that "select all empty" means all the white squares because you only want to see the red lines so they can guide you to the primary structure. If there was also a slider as Karen suggested, the determination of green or white would be made by the slider so that all of the excess information below the slider threshold setting would be considered white squares yielding red lines.

Joined: 11/10/2007
Groups: Window Group

I think 'select all empty' would select the green squares which don't have contacts showing? Would it be useful to select all the white squares?

Joined: 09/21/2011

I don't see a need to select all the white squares. The green squares without contacts, or all green should be fine.

Joined: 09/24/2012
Groups: Go Science

Summary (and my preferences):

1-select all green
2-Karen's slider related to heat
3-select all green without contact ('"all empty" or "all red"?)
4-surface selection of several points together on screen (square or circle)
5-jeff's two grey cross-hair lines stay in place if we want (e.g. when shift clicking)
6-band strength choice: default or "relative to heat"
OR better:
7-a slider for band strength of new selected (so that we can combine selections, band them, new selection, band them with other strength ...)
OR even better:

8-Modes: "select" mode and "band" mode. On band mode, we can select what we want, and selectively band selected contacts with common band attributes This tool could even be used (with n°4) to quickly select a lot of existing bands and change their attributes. The "contact map" would then be a permanent tool for all puzzles (with heat only when available). It could even be interesting to be able to add our own "heat" on non contact puzzles, in order to design our own wanted structure using the contact map tool.

9- and a special symbol for banded pairs (a way to identify and then select all existing bands ! then use tool n°8). For example a circle in the square.

Joined: 09/24/2012
Groups: Go Science

Thanks !

The new contact map tool is quite good. If I'm right, the following points are now possible with the new tool: 1-3-5-8

The other suggestions are "nice to have". May be wait a little bit to evaluate the current update before to consider these ones:

2-Karen's slider related to heat
4-surface selection of several points together on screen (square or circle)

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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, RosettaCommons