Ability to select specific section of protein and hide the rest of the protein completely.

Case number:699969-994464
Topic:General
Opened by:ComputerMage
Status:Open
Type:Suggestion
Opened on:Sunday, February 3, 2013 - 14:11
Last modified:Wednesday, March 27, 2013 - 19:35

Hi guys/gals,

I want to have ability to select specific fragment of protein and hide the rest of the protein completely.
So it's like to work with shorter protein to fold it to the proper structure, and then to add the additional block to fold. It's like simulation of exit zone of the ribosome. Or like working with the folding of specific fragment. This is very easy to implement but it will allow to fold more intuitively to the people.

All the Best!
Sergey.

(Sun, 02/03/2013 - 14:11  |  11 comments)


tamirh's picture
User offline. Last seen 6 years 19 weeks ago. Offline
Joined: 05/11/2012

This doesn't hide the rest of the protein, but have you tried using cutpoints? That will allow you to fold only pieces of the protein and then reassemble them later.

Joined: 11/17/2009
Groups: Russian team

Of course I did!

The only issue with that that cutpoints also behave as a bands that are trying to pull all parts together and it is negates all efforts.

tamirh's picture
User offline. Last seen 6 years 19 weeks ago. Offline
Joined: 05/11/2012

Selection Interface

If you are using the selection interface (Menu -> Selection Interface) you can select parts of the protein. Pull, wiggle, shake etc. will then only apply to the selection portions.

That should address the issue you mentioned if I'm understanding you correctly. If not, let me know what it is you're trying to do.

Joined: 08/24/2011

I learned last week that's what the "enable backbone constraints" checkbox is for: it disables the band effect. Thanks again to drumpeter18yrs9yrs btw.

I noticed too that if we do a sphere selection in the void, some sort of mist appears, but it works backwards: it hides the inside of the protein. Maybe that's just another wine bug, but if not and that mist was inverted that would be perfect.

tamirh's picture
User offline. Last seen 6 years 19 weeks ago. Offline
Joined: 05/11/2012

Thanks Jean-Bob, forgot about that flag (=

Joined: 11/17/2009
Groups: Russian team

Cool! Thanks for a tips. That stuff about backbone constraints I didn't know. I always wondered what it's doing.

Joined: 09/21/2011
Groups: Void Crushers

Beware when using that flag. The backbone scores of segments used in a wiggle can get very bad when doing a wiggle.

Joined: 11/17/2009
Groups: Russian team

Ok. In overall my idea is to start a wiggle and rebuild from small piece ( about 5 segments) to shake and wiggle it, and then to start to add more segments to it - some kind of simulation what happens to the protein when it leaves the ribosomes' exit hole.

Joined: 11/17/2009
Groups: Russian team

Also I would love to have ability to use the cuts in the scripts so I can simulate it in the script. ;)

Joined: 11/17/2009
Groups: Russian team

Also, the backbone constraint is not obeyed by cuts, they still work like a a bands with 1.5 band strength.

My whole point was is to work with part of the protein (read domain) and to stabilize it and then to start add some other segments (one-by-one) to wiggle them so they will be more better adjusted to the domain.

brow42's picture
User offline. Last seen 10 hours 42 min ago. Offline
Joined: 09/19/2011
Groups: None

Disabling Backbone Constraints definitely turns off the cut bands. I sometimes check the box and then add my own bands for a weaker pull.

DBC *MAY* also turn off invisible strong bands where there aren't cuts. Usually the backbone holds together anyways from just the energy gradient, but using bands and wiggle, I've had backbone scores plummet where there are no cuts.

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