How to improve the structure of the inner residues of a protein while keeping the end residues fixed?

Case number:845813-2006343
Topic:Game: Tools
Opened by:jeff101
Status:Open
Type:Question
Opened on:Wednesday, December 26, 2018 - 09:47
Last modified:Thursday, January 10, 2019 - 08:23
I am trying to make a recipe that improves the structure 
of the inner residues of the protein while keeping the 
end residues of the protein fixed. So far things aren't 
working as expected. Say the protein is 100 residues long 
and I want to improve the structure of residues 30-40. 
If I select segments 30-40 and use tools like rebuild, 
shake, or wiggle sidechains, only residues 30-40 move, 
which is what I want. Meanwhile, selecting residues 30-40, 
freezing the rest, and using wiggle backbone or wiggle both 
backbone & sidechains makes residues 30-40 move, as desired, 
but it also makes residues 41-100 move as a unit or rigid 
body, which I don't want to happen. I want residues 41-100 
to stay fixed in place. I have tried adding some zero-length 
bands with strength 10 to residues 41-100, but residues 
41-100 still move more than I want when residues 30-40 have 
their backbone wiggled. I suppose I could add many more 
strength 10 bands to keep residues 41-100 fixed in place, 
but this doesn't seem ideal. Is there a more elegant 
solution? Like what is keeping residues 1-29 fixed in 
place? Is there a way to make segments 1-29 move instead 
of segments 41-100?
(Wed, 12/26/2018 - 09:47  |  6 comments)


spvincent's picture
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Groups: Contenders

Might using structure.LocalWiggleSelected () instead of structure.WiggleSelected () work?

Susume's picture
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Joined: 10/02/2011

In view menu, turn on Pins, and look for the purple pin on the protein. It is possible that dragging it onto residue 41 and then repeating your steps of freezing 41-100 and wiggling 30-40 will now leave 41-100 in place and only move 1-40. I have not quite figured out how freeze and pins interact, but pins are in theory supposed to determine which end of the protein stays fixed in space while the other end moves.

If you have one or more cuts in the protein, each piece will have its own pin. When there are no cuts, there is just one pin for the whole protein.

jeff101's picture
User offline. Last seen 15 hours 47 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

Thanks Susume & spvincent.

I viewed the pins. I saw one pin at the high #'d end
pointing to the right. I tried moving this pin to the
low #'d end (gave same behavior as above). Then I tried
right-clicking on the pin so it pointed down. With the
pin at the low #'d end & pointing down, I got the same
behavior as above. With the pin at the high #'d end &
pointing down, segments 1-29 move instead of segments
41-100.

Maybe I need to use a cut so I can have one pin for
each end of the protein.

One of my clients is newer than the other clients.
Have recent client updates changed how the pins
affect things?

Are there any LUA commands that will add, remove,
or move pins? Are there any LUA commands that will
make pins change between pointing to the right and
pointing down?

Maybe later I will try LocalWiggleSelected instead
of WiggleSelected.

robgee's picture
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Joined: 07/26/2013

In relation to pins and Lua commands.
AFAIK, not implemented yet.
https://fold.it/portal/node/2005040

jeff101's picture
User offline. Last seen 15 hours 47 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

One trick I haven't tried yet is to just add more strength 10
zero-length bands to the regions I want to stay fixed. If that
isn't enough, I could replace each zero-length band with 2 or more
very long bands to space. For 2 bands, I could have them go in
opposite directions from the target position. For 3 bands, I could
have them go outward from the target position in 3 coplanar
directions 120 degrees apart (like each band would point to a
different vertex of an equilateral triangle centered on the target
position). For 4 bands, I could have them go outward from the
target position into space in 4 different directions pointing to
the 4 vertices of a tetrahedron centered on the target position
(this would be like aiming the 4 bands at 4 non-adjacent corners
of a cube centered on the target position). Nevertheless, the more
bands needed, the less elegant this solution seems.

jeff101's picture
User offline. Last seen 15 hours 47 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

To select a small region of the protein to leave unfrozen and able to
move while selecting a large region of the protein to freeze and hold
fixed, I looked at the LUA commands available. It was helpful that the
command freeze.FreezeSelected(bb,sc) would freeze the backbones if bb
was true and the sidechains if sc was true. I was disappointed that the
command freeze.UnfreezeSelected(bb,sc) did not exist. I also wondered
if freeze.Freeze(indx,true,false) and freeze.Unfreeze(indx,false,true)
would behave the same as each other. I also thought it would be useful
if selection.DeselectRange(indx1,indx2) and selection.Reverse() existed.
selection.Reverse() would just go through all the residues, changing
selected ones to unselected ones, and changing unselected ones to selected
ones. http://foldit.wikia.com/wiki/Foldit_Lua_Functions gives more details.

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