I think what's causing me problems is that the beta sheet strands are twisted and I can't untwist them. I just want to pick them up and do it with my fingers. There should be a button that says "straighten out sheet regions". It's infuriating!!!
You can straighten out them, using the new inteface (GUI)
double-click on a sheet, it should be marked completely blue, and some arrows will appear.
Above the arrows, there is a knob, which you will have to keep pushing.
Look, I marked the knob red.
Knob for straighten out sheets: Shows up if a sheet is selected
levinthal, there is a tool that allows you to straighten sheets. But you have to be careful how to use it and often rebuilding the entire sheet is a better option.
Straightening sheets:
If you are in original interface mode, right-click on the sheet, select "Tweak", then click and hold on one of the purple balls and wait until your sheet is normalized.
If you are in selection mode, double-click on your sheet so that the sheet and the surrounding loops are selected, then proceed as above.
Note that straightening a sheet often causes the surrounding loops to be twisted and getting low in score. These regions have to be rebuilt manually afterwards.
Rebuilding sheets:
In original interface mode, right-click on your sheet and press "Rebuild", in selection mode you would double-click the sheet and then press "Rebuild". Wait until a sheet is generated that does not have the twists in it that you wanted to remove.
OK I'm clicking on purple balls but nothing is moving. clicking on the arrows makes the whole sheet rotate a few degrees…
And above these arrows you use to rotate, there is a knob (purple balls).
I'm just creating a script to do this.
At the moment, we can't download them, but past them as text.
are also lost on me I'm afraid :-) Don't worry I have made some kind of breakthrough with freezing and rebuilding…
I dragged everything so it perfecly overlaid the guide, rebuilt a few bits to tidy them up, made loads of hydrogen bonds, cemented it with purple bands, then did shake and wiggle and it just tries to fling itself apart again. I'm giving up before I trash the computer.
One common reason that nothing moves when you hold down the purple button is that the loops attached to either side of the structure you're working on are too short. This is because the procedure for straightening those structure work by bending the amino acid residues as necessary– and if there isn't enough space as "cushion," it might be impossible to do so.