Do you use the Align or Refine Align buttons?

Case number:699969-995563
Opened by:jflat06
Opened on:Wednesday, July 17, 2013 - 19:28
Last modified:Saturday, July 20, 2013 - 18:39

Hey everyone,

I am looking into simplifying the electron density panel, and I am wondering how much people use the align and refine align buttons.

The Align button is nearly useless in the untrimmed maps that we have been posting since there are bits to the cloud that don't belong (and therefore, it cant match the protein). However, I can still see this potentially being useful to just move the density into the center of the cloud. Thoughts on this?

The Refine Align button also seems like it isn't as useful anymore. Originally this was very useful, since the density scoring wasn't part of the score function. However, now that you're rewarded for your density fit, Wiggle now will 'settle' the protein into the cloud automatically. Does anyone find this button useful beyond just spamming it to get a few more points?


(Wed, 07/17/2013 - 19:28  |  11 comments)

Joined: 04/15/2012
Groups: Beta Folders

I use the align button to get it into the cloud, yes. I do that occasionally use it to try to use the cloud, as we have it, and it sometimes gives extra points after settling. Refine alignment button doesn't do anything, so I don't use that.

marie_s's picture
User offline. Last seen 1 year 40 weeks ago. Offline
Joined: 05/18/2008
Groups: None

Never, I move the protein with the move tool.

Angus's picture
User offline. Last seen 8 hours 18 min ago. Offline
Joined: 06/04/2008
Groups: Beta Folders

I only use the Align button when I can't find the cloud. Never use the other one, doesn't do anything.

Joined: 09/21/2011
Groups: Void Crushers

Same here, just to find the cloud. Other than that it is not useful at all. It spoils the position unless you are very near the solution, but even in that case you loose when you use it.
I have a question for you about the new tool you are working on for ED.
When I look at the pictures you put into chat it looks like the tool hides everything of the cloud outside the protein. In my opinion it would be more useful when it shows also the cloud just outside of the protein maybe everything within a certain distance (3?), perhaps even settable.

jflat06's picture
User offline. Last seen 9 hours 41 min ago. Offline
Joined: 09/29/2010
Groups: Window Group

That's actually how it works. You can set a threshold for how far away from the protein to show with a slider pop-up.

Eventually, my plan is to make it so that this tool can show you the repeated density as well, so that you can fit to parts of density that cross the cell boundaries.

Joined: 09/21/2011
Groups: Void Crushers

Cant wait for that tool. I like it already without having seen it in action. Big :-)

alwen's picture
User offline. Last seen 41 weeks 5 days ago. Offline
Joined: 10/03/2011

The only time I use Align is early in the puzzle when I've lost the density off the screen or into the fog. That is, I use it like Q to locate the density cloud.

I use the Refine alignment a lot. For example I use Move and drag the protein a very small distance, then Refine, then wiggle. Often that changes the fit to the cloud just enough that my score will jump. I use Refine after a rebuild, following shake/wiggle.

brow42's picture
User offline. Last seen 1 year 36 weeks ago. Offline
Joined: 09/19/2011
Groups: None

I never use align or refine align anymore. The extra other/density contribution to the score makes the density just suck the protein into the cloud by wiggling or rebuild scripting. Likewise, the move tool suffices for perturbing the score surface to sort of 'nudge' everything.

mimi's picture
User offline. Last seen 3 weeks 6 days ago. Offline
Joined: 11/17/2008
Groups: Contenders

I don't use them either because they don't seem to do what you would expect them to do.
Whenever I have got a protein into a position in an ED cloud which looks good (to me)
using either button usually moves it to a completely different and lower scoring position
- so not really much help

alcor29's picture
User offline. Last seen 19 hours 35 min ago. Offline
Joined: 11/16/2012

I just got over 100 points using the refine button. It doesn't happen often, but that may be my lack of skill. I wish you wouldn't do away with it. I agree with Alwen.

Joined: 09/21/2011

yeah, i use it to find the cloud. otherwise i don't use it.


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, Boehringer Ingelheim, RosettaCommons