Try this:
PyMOL>super PDBfile1////CA, PDBfile2////CA
PyMOL>Save PDBfile1.pdb, PDBfile1
PyMOL>Save PDBfile2.pdb, PDBfile2
Explanation:
The first line aligns the alpha carbons of the two files.I assume you
have loaded the two files in advance. The RMSD will appear on the screen
as output.The second and third lines take the Pymol objects PDBfile1 and
PDBfile2 and saves their newly aligned coordinates in pdb format.You
might want to look up the align and the super commands in the wiki.Super
is a better version of align.
Super iterates, removing outlier atoms progressively until it finds no
further statistical reason to remove any more.If you want only an
alignment that uses all CA atoms, you can restrict the calculation to
one iteration as follows:
PyMOL>super PDBfile1////CA, PDBfile2////CA, cycles=0
Then save the aligned files as above.
Peter Kahn
On 9/10/2014 12:11 AM, Amita Rani Sahoo wrote:
Dear Pymol users,
I want to calculate backbone RMSD of proteins having two different
conformations (For example 2RH1 and 1F88). With the align command it
calculates the executive RMSD, but i need backbone RMSD. Please advise
something.
Regards
*Amita *
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