[MMTK] how to calculate RMS value for residue

Fan Gao Gao.Fan@mayo.edu
Mon, 14 Oct 2002 19:42:21 -0500


--=====================_36064948==_.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed

Hi, all
I found MMTK can calculate RMS values between peptide chains (in the 
Examples of MMTK). But I am not sure how to calculate residue based RMS value ?
I tried the following:
configuration1 = PDBConfiguration('1.pdb')
configuration1 = PDBConfiguration('2.pdb')
residue_configuration1 = configuration1.residues[0]
residue_configuration2 = configuration2.residues[0]
However, I don't know what to do next.  ***1.pdb and 2.pdb are different 
proteins
Does anyone know how to do that?

Thanks for the help.

Fan


----------
Fan Gao

Dept. of Biomedical Engineering
Receptor Biology Lab
Medical Science Building 1-155
Mayo Clinic
Work Phone: 507-264-8461

----------

--=====================_36064948==_.ALT
Content-Type: text/html; charset="us-ascii"

<html>
Hi, all<br>
I found MMTK can calculate RMS values between peptide chains (in the
Examples of MMTK). But I am not sure how to calculate residue based RMS
value ?<br>
I tried the following:<br>
configuration1 = PDBConfiguration('1.pdb')<br>
configuration1 = PDBConfiguration('2.pdb')<br>
residue_configuration1 = configuration1.residues[0] <br>
residue_configuration2 = configuration2.residues[0]<br>
However, I don't know what to do next.&nbsp; ***1.pdb and 2.pdb are
different proteins<br>
Does anyone know how to do that?<br><br>
Thanks for the help.<br><br>
Fan<br>
<x-sigsep><p></x-sigsep>
<hr>
Fan Gao<br><br>
Dept. of Biomedical Engineering<br>
Receptor Biology Lab<br>
Medical Science Building 1-155<br>
Mayo Clinic<br>
Work Phone: 507-264-8461<br>
<hr>
</html>

--=====================_36064948==_.ALT--