CARNAL RMS fits have large >50A deviations!

From: samantha hughes <>
Date: Thu 21 Oct 1999 10:28:10 +0100

Hi all,

I have performed an RMS fit using CARNAL on two average
structures from 100ps of dynamics. I have fitted one RMS
structure to the other RMS structure on a "per residue" basis. I
don't expect to see huge structural variations, and in the main
these are not observed, with the RMS value fluctuating around 4A.
There are some unexpectedly large values though,eg 50A for a Mg
ion present. I have checked the PDB files for these 2 average
structures and find that the Mg ion has very similar coordinates
in both files. So why the 50A deviation ?

Any ideas anyone ? The two files have the same number of
residues, but different numbers of atoms. The residue in question
is numbered the same in both files.

Any help would be greatly appreciated.

Samantha Hughes

Time's fun when you're having flies.
   -Kermit the Frog (Jim Henson)
Received on Thu Oct 21 1999 - 02:28:10 PDT
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