Thanks Yang Ye! I will look into this further. Thanks for the program, I'm
sure that will save me much time.
Russell Green
On 6/11/07, Yang Ye <[EMAIL PROTECTED]> 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]
}
}
}
----- Original Message ----
From: Russell Green <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Tuesday, June 12, 2007 2:17:45 AM
Subject: [gmx-users] dPCA "atoms"
Dear Gromacs community,
I've been using the PCA analysis in dihedral space for a chain of my
protein of interest. I made a script to collect the atom quadruplets
corresponding to the phi and psi angles and output them to an index file. I
followed the steps in the paper manual and everything worked as it should;
however, is there any way to relate the dihedral PCA information to each
residue that contributed to the analysis? As it stands, my dummy reference
file contains 715 "atoms" but the analysis was done for about 536 residues
so that's 3 atoms per residue helping to define the dihedral angles. Could
someone please provide some suggestions or more insight? I've searched the
net and the mailing list but have found no information regarding my
question.
Thanks in advance,
Russell Green
UAB Undergraduate Researcher
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