<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">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.<br><br>BEGIN {<br> i=0<br> grid_num=40.0<br><br> x_max=0.0<br> y_max=0.0<br> x_min=0.0<br> y_min=0.0<br><br> temp=300<br>
dkt=8.31/1000.0*temp/4.182<br>}<br><br>{<br> x[i]=$1<br> y[i]=$2<br><br> if ($1>x_max) x_max=$1<br> if ($2>y_max) y_max=$2<br> if ($1<x_min) x_min=$1<br> if ($2<y_min) y_min=$2<br> i++<br>}<br><br>END {<br> pt_num=i<br><br> grid_x_size=(x_max-x_min)/grid_num<br> grid_y_size=(y_max-y_min)/grid_num<br><br> dm=0<br> for(i=0;i<pt_num;i++) {<br> grid[(int((x[i]-x_min)/grid_x_size)), (int((y[i]-y_min)/grid_y_size))]++<br> g=grid[(int((x[i]-x_min)/grid_x_size)), (int((y[i]-y_min)/grid_y_size))]<br> if(dm<g) { dm=g; }<br> }<br><br> mm=0;<br> for(i=0;i<grid_num;i++) {<br> for(j=0;j<grid_num;j++) {<br>
if(grid[i,j]!="") { grid[i,j]=dkt*log(dm/grid[i,j]); if (grid[i,j]>mm) {mm=grid[i,j];} }<br> }<br> }<br><br> for(i=0;i<grid_num;i++) {<br> for(j=0;j<grid_num;j++) {<br> if(grid[i,j]=="") { grid[i,j]=mm+0.01 }<br> print x_min+(i+0.5)*grid_x_size " " y_min+(j+0.5)*grid_y_size " " grid[i,j]<br> }<br> }<br>}<br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Russell Green <russellwgreen@gmail.com><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Tuesday, June 12, 2007 2:17:45 AM<br>Subject: [gmx-users] dPCA "atoms"<br><br><div>Dear Gromacs community,</div>
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<div> 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
<font style="background-color: rgb(255, 255, 255);">more insight? I've searched the net and the mailing list but have found no information regarding my question.</font></div>
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<div>Thanks in advance,</div>
<div>Russell Green</div>
<div>UAB Undergraduate Researcher</div>
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