# [gmx-users] dPCA "atoms"

Yang Ye leafyoung at yahoo.com
Mon Jun 11 20:35:50 CEST 2007

```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 <russellwgreen at gmail.com>
To: Discussion list for GROMACS users <gmx-users at 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.

Russell Green

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