Naming of phosphate oxygens

Mary Coventry coventry at
Mon Nov 27 20:13:18 EST 1995

In article <491eru$rd9 at>, slickers at (Peter
Slickers) wrote:

> Because I want to calculate true rms distances between a crystral 
> structure form the Brookhaven database and a modell. I have tried 
> this for the drew-dickerson dodecamer '1BNA' using InsightII. 
> In the structure build with Insight the two phosphate oxygens are 
> pointing just to the opposite direction as in the crystal structure. 
> If I now calculate the rms distance between the two structures I 
> get a wrong value because the atoms in the two structures are 
> aligned according to their ordering in the pdb files and _not_
> according to their chiral positions.   
InsightII does't care about atom's names when it calculates rmsd. Even if
you will give correct names for atoms in both structures, rmsd can be
different. You should reshuffle lines in pdb (or *.car, whatever) files.
For example, if you have CORRECT names for O1P and O2P but in one file you
have them ordered like 
P;O1P;O2P and P;O2P;O1P in second one, the rmsd calculation will be wrong.
I had this problem before and the only solution was to write a short
program to rearrange atoms in one of the files. I can send program if you
need it and  if I will be able to find it in my messy stuff. 

Good luck, Oleg Fedoroff.

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