Sidechain positions

Started by reed

reed Lv 1

This suggestion was mentioned in the "sidechain flipping" article on the wiki, but I'll repeat it here.

To see the possible sidechain positions, right now we have to grab the sidechain and wave it around.  For example, proline might have 1-2 positions and tryptophan might have 5-6 positions.  To see all of these, sometimes I need to turn the protein around to make sureI found all of them.  For the large juicy sidechains, it's not always clear at first that I've found every position.

It would be better if it was easier to see and access the possible positions (rotamers?) of each sidechain.  For example, clicking (shift-click, ctrl-click?) on a sidechain could bring up discrete buttons for each position, or maybe a slider which slides through each position?   

Example:  We click on a long, squiggly sidechain and a slider with 4 positions pops up.  We quickly slide through the 4 positions and watch the score change for each one.  We stop on one that looks promising and start wiggling.

spvincent Lv 1

This exact feature (with a slider to control rotamer positions) used to be in FoldIt. I agree it would be good if it were reinstated.

Seagat2011 Lv 1

Agreed. We need an interface or slider-like tool to see what the sidechain rotameters would look like, and to select between them.

Madde Lv 1

In the new Selection Interface you can select a sidechain and then use the left and right arrow keys on your keyboard to flip through the different positions.

Crashguard303 Lv 1

Yes, they are called snap positions.
If you mouse over a segment and press TAB, it will show you the segment number (and more).

Using scripts, then you can change them by do_sidechain_snap(segment number, position).

get_sidechain_snap_count(segment number) will show you how many positions are possible for this segment.

TheGUmmer Lv 1

When looping through the sidechain snap counts in your code watch out because the count can change in mid loop. It will cause an error and your code will stop.