Yang Ye wrote:
As what we normally do with dPCA, after obtaining the 2D projection of
first and second principle, we make it into a 3D plot of free energy
surface. The awk program is provided below to do such conversion. On
this surface, we can located regions with low free energy and this leads
us to go back to 1D projection to locate which frames are inside the
regions. Clustering or averaging may apply to all the frames found in
one region. So, in the end, structure are found inside the trajectory
for closer inspection.
BEGIN {
i=0
grid_num=40.0
x_max=0.0
y_max=0.0
x_min=0.0
y_min=0.0
temp=300
dkt=8.31/1000.0*temp/4.182
}
{
x[i]=$1
y[i]=$2
if ($1>x_max) x_max=$1
if ($2>y_max) y_max=$2
if ($1<x_min) x_min=$1
if ($2<y_min) y_min=$2
i++
}
END {
pt_num=i
grid_x_size=(x_max-x_min)/grid_num
grid_y_size=(y_max-y_min)/grid_num
dm=0
for(i=0;i<pt_num;i++) {
grid[(int((x[i]-x_min)/grid_x_size)),
(int((y[i]-y_min)/grid_y_size))]++
g=grid[(int((x[i]-x_min)/grid_x_size)),
(int((y[i]-y_min)/grid_y_size))]
if(dm<g) { dm=g; }
}
mm=0;
for(i=0;i<grid_num;i++) {
for(j=0;j<grid_num;j++) {
if(grid[i,j]!="") { grid[i,j]=dkt*log(dm/grid[i,j]); if
(grid[i,j]>mm) {mm=grid[i,j];} }
}
}
for(i=0;i<grid_num;i++) {
for(j=0;j<grid_num;j++) {
if(grid[i,j]=="") { grid[i,j]=mm+0.01 }
print x_min+(i+0.5)*grid_x_size " " y_min+(j+0.5)*grid_y_size "
" grid[i,j]
}
}
}
you can also use g_sham to make energy landscapes. however you still
have to make the connection to 3D space which is not all trivial.
potential barriers in dihedral space may be trivial in 3D space due to
vanderwaals interactions. please do also use normal PCA and compare
results, in particular the interpretation in terms of structure.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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