Hi,
In order to get the RMSD of a specific region after fitting on another
region you need two rms commands. Say your reference is residues
1-100, and you want the rms of residues 50-55:
reference refstruct.rst7
rms reference :1-100
rms reference :50-55 nofit out rmsd.dat
The first rms command performs the best fit, then the second rms
command calculates the rmsd you want without changing the fit from the
first rms command.
-Dan
On Mon, Feb 7, 2011 at 1:50 PM, Rahul Banerjee
<rahul.banerjee.chemistry.msu.edu> wrote:
> Dear All,
>
> How can I calculate RMSD for a given region in the protein by aligning the core structure with a given crystal structure? I have made some changes in the protein (mutation) and due to that some loop regions are likely to become flexible. Where the core structure is unlikely to move. I have crystal structure of the mutated form as well, that I can use as reference in the alignment process.
>
> Thanking you.
>
> With best regards,
> Rahul
>
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Received on Tue Feb 08 2011 - 08:30:02 PST
