[BiO BB] Help with RMSD calculation

Shameer Khadar skhadar at gmail.com
Wed Aug 2 02:45:45 EDT 2006

Hi Raj,

You can do it even with out scripts/algos !
Try using any standard protein visualisation tool like Chimera or VMD both
of them have option for
RMSD calculation (no matter if it is a fragment or a full proteins). STRAP -
Java Web Start  (http://www.charite.de/bioinf/strap/) will be another easy
option, where you can do this.

Shameer Khadar
Prof. R. Sowdhamini's Lab

On 8/2/06, Raj <rajkumar.bondugula at gmail.com> wrote:
> Does anyone have a script or algorithm that can calculate the minimum
> RMSD if C-alpha co-ordinates of two protein fragments are given? I
> mean, the algorithm should rotate and translate the first set of
> co-ordinates until it results in minimum RMSD with the second set of
> points.
> Thank you,
> Raj
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