User:Karsten Theis/Rigid body interpolation
From Proteopedia
(Difference between revisions)
| Line 40: | Line 40: | ||
{all}.xyz = @original | {all}.xyz = @original | ||
progress = 0.05 * i | progress = 0.05 * i | ||
| - | for (var j FROM [1,sel.length) { | + | for (var j FROM [1,sel.length]) { |
s = sel[j] | s = sel[j] | ||
a = anch[j] | a = anch[j] | ||
| - | for (var c in [{ | + | for (var c in [{chain='A'},{chain='B'},{chain='C'}]) { |
define sel1 1.1 and @s and @c | define sel1 1.1 and @s and @c | ||
define sel2 1.2 and @s and @c | define sel2 1.2 and @s and @c | ||
| Line 53: | Line 53: | ||
} | } | ||
delay 1.0 | delay 1.0 | ||
| + | } | ||
| + | |||
| + | |||
# fname = "morph" + i + ".pdb" | # fname = "morph" + i + ".pdb" | ||
# select 1.1 | # select 1.1 | ||
# write @fname | # write @fname | ||
| - | + | ||
| - | + | ||
| - | + | ||
</nowiki> | </nowiki> | ||
Revision as of 14:51, 7 March 2021
This page shows a way to superpose two rigid bodies so that they both have the same rotation, and they are translated such that a common anchor (center of mass, given atom) is in the same location.
The entire coordinates are copies first so that you can play around with the parameters and then reset the coordinates. The starting point is a structure with two models containing the same atoms in the same order, but with different coordinates.
function linear(progress) {
coord1 = {sel1}.xyz.all
coord2 = {sel2}.xyz.all
len = coord1.length
ssergorp = 1 - progress
for (var i FROM [1,len]) {coord1[i] = (coord2[i] * progress + coord1[i] * ssergorp)}
{sel1}.xyz = @coord1
}
function rigid(progress) {
fourbyfour = compare({sel1}, {sel2})
total_quat = quaternion(@fourbyfour%1)
theta = total_quat %"theta"
ax = total_quat %"vector"
if (theta > 160 and theta < 170) total_quat = quaternion(ax, 360 - theta)
ssergorp = 1 - progress
quat1 = total_quat * progress
quat2 = total_quat * ssergorp * -1
anchorpos = {anch2}.xyz * progress + {anch1}.xyz * ssergorp
select sel1
rotateselected @quat1 molecular
transl1 = anchorpos - {anch1}.xyz
translateselected @transl1
select sel2
rotateselected @quat2 molecular
transl2 = anchorpos - {anch2}.xyz
translateselected @transl2
}
sel = [{912-984},{1125-1162},{not (1125-1162 or 912-984)}]
anch = [{984},{984},{not (1125-1162 or 912-984)}]
original = {all}.xyz.all
for (var i FROM [1,20]) {
{all}.xyz = @original
progress = 0.05 * i
for (var j FROM [1,sel.length]) {
s = sel[j]
a = anch[j]
for (var c in [{chain='A'},{chain='B'},{chain='C'}]) {
define sel1 1.1 and @s and @c
define sel2 1.2 and @s and @c
define anch1 1.1 and @a and @c
define anch2 1.2 and @a and @c
rigid(progress)
linear(progress)
}
}
delay 1.0
}
# fname = "morph" + i + ".pdb"
# select 1.1
# write @fname
Example
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