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Friday, March 27, 2009
How I Fold Protein
Kia Ora,
The first thing I do, when the New Puzzle first appears, is to either global "Shake." or "Wiggle.", once it has finished, I will reset the new puzzle just to see which starting point is going to give the best result.
Lately, I have found that before I start the first shake or wiggle, is to left click and hold on any sidechain that is bent, curled over or not looking like its in the best position ( intution helps eventually ) and pull it manually into a straight as possible position that I can. *pull it so it has not bends in it* then do the wiggle first, then shake it.
I will always click on global wiggle, after anything I do, and wait a few seconds to a minute, just to make sure it has finished and gone as far as possible, before I make the next step... which is to shake it.
I can Pull(left button click, on the protein backbone for a split second or three, moving the cursor into the white area area away from or into the protein, or into different directions until something moves.) and then I let go of the left button, so that it makes the protein move all by itself, (if it doesn't) I try pulling from another angle. Or even spinning the protein around until I find a point that it will wiggle on it's own, then eventually stall... or until the protein moves out of shape, but not too much.(much if no more points go upwards) or just enough to make one or two sidechains move, then once again "click on global wiggle."
I will then once again shake, then global wiggle again and shake and global wiggle till it won't. I don't have to BAND to get most puzzles into the top 20, but I do band if it has red/brown lines between the backbone. If the red/brown lines are there lock all, and then band over the red/brown lines and unlock JUST the areas underneath the red/brown lines. if nothing happens on LOCAL WIGGLE, I will unlock the next segments either side of the redlined/brown backbone.
I will sometimes assist the wiggle by clicking(double clicking, or clicking on the sidechains and/or forcing it somewhere myself) by clicking on every sidechain possible whiles its moving to give it a hand sometimes works. I randomly select ones, OR THREE DIFFERENT SIDECHAINS minimum, or just the ones with colours that are the same. all red, all orange, Blue, brown or green, depending on my mood and if the scores goes up, I will UNDO or Restore best if after a few goes nothing goes upwards, but sometimes I can sit and do the process 10 times and on the tenth time, the points go up and past some of the other players without me even knowing whats going on until I hear the rank up tone. wooohoooo. that's it.
REBUILDING - two different ways I rebuild. I can lock either side of two, three or four open segements, then right click and choose to rebuild it, waiting for a few seconds for it to move, then shake and wiggle after I stopped it where it "looks" like its in a more natural position... USE THE UNDO FEATURE AND RESTORE BEST often ok!
These are the basics ! You need to get used to trying out all these skills, tips and Tools yourself! try different combinations to see what works and what doesn't... everyones styles will differ. This works for me.
If you look and work on the browner areas first,(sometimes including a greenish segment area too) the darker green resulting segment area means you got it pretty good, then move around the protein and continue the same kind of methods, then shake and wiggle it out.
To be continued...
Copyrights 2009 Aotearoa - Land of the Long White Cloud - Renton Innes - Auckland - Phone 0064 211 81 63 81
All Rights Reserved. Ex Manager FREEDOM FOLDERS - presently Richard Dawkins Foundation, Anthropic Dreams.
You are welcome to join our team for more personal support and advice. Kia Kaha. Renton.
The first thing I do, when the New Puzzle first appears, is to either global "Shake." or "Wiggle.", once it has finished, I will reset the new puzzle just to see which starting point is going to give the best result.
Lately, I have found that before I start the first shake or wiggle, is to left click and hold on any sidechain that is bent, curled over or not looking like its in the best position ( intution helps eventually ) and pull it manually into a straight as possible position that I can. *pull it so it has not bends in it* then do the wiggle first, then shake it.
I will always click on global wiggle, after anything I do, and wait a few seconds to a minute, just to make sure it has finished and gone as far as possible, before I make the next step... which is to shake it.
I can Pull(left button click, on the protein backbone for a split second or three, moving the cursor into the white area area away from or into the protein, or into different directions until something moves.) and then I let go of the left button, so that it makes the protein move all by itself, (if it doesn't) I try pulling from another angle. Or even spinning the protein around until I find a point that it will wiggle on it's own, then eventually stall... or until the protein moves out of shape, but not too much.(much if no more points go upwards) or just enough to make one or two sidechains move, then once again "click on global wiggle."
I will then once again shake, then global wiggle again and shake and global wiggle till it won't. I don't have to BAND to get most puzzles into the top 20, but I do band if it has red/brown lines between the backbone. If the red/brown lines are there lock all, and then band over the red/brown lines and unlock JUST the areas underneath the red/brown lines. if nothing happens on LOCAL WIGGLE, I will unlock the next segments either side of the redlined/brown backbone.
I will sometimes assist the wiggle by clicking(double clicking, or clicking on the sidechains and/or forcing it somewhere myself) by clicking on every sidechain possible whiles its moving to give it a hand sometimes works. I randomly select ones, OR THREE DIFFERENT SIDECHAINS minimum, or just the ones with colours that are the same. all red, all orange, Blue, brown or green, depending on my mood and if the scores goes up, I will UNDO or Restore best if after a few goes nothing goes upwards, but sometimes I can sit and do the process 10 times and on the tenth time, the points go up and past some of the other players without me even knowing whats going on until I hear the rank up tone. wooohoooo. that's it.
REBUILDING - two different ways I rebuild. I can lock either side of two, three or four open segements, then right click and choose to rebuild it, waiting for a few seconds for it to move, then shake and wiggle after I stopped it where it "looks" like its in a more natural position... USE THE UNDO FEATURE AND RESTORE BEST often ok!
These are the basics ! You need to get used to trying out all these skills, tips and Tools yourself! try different combinations to see what works and what doesn't... everyones styles will differ. This works for me.
If you look and work on the browner areas first,(sometimes including a greenish segment area too) the darker green resulting segment area means you got it pretty good, then move around the protein and continue the same kind of methods, then shake and wiggle it out.
To be continued...
Copyrights 2009 Aotearoa - Land of the Long White Cloud - Renton Innes - Auckland - Phone 0064 211 81 63 81
All Rights Reserved. Ex Manager FREEDOM FOLDERS - presently Richard Dawkins Foundation, Anthropic Dreams.
You are welcome to join our team for more personal support and advice. Kia Kaha. Renton.
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