[Chimera-users] [chimera-dev] Calculating RMSD
meng at cgl.ucsf.edu
Fri Jan 15 10:56:19 PST 2010
I'll CC the chimera-users at cgl.ucsf.edu list -- that address is
better for general Chimera "user" questions, while chimera-dev is
more for "programmer" questions, i.e. involving python or other code.
The "rmsd" command does not automatically use serial number to pair
the atoms. You can control the order by specifying the residues and
their atoms in the command. Of course, that can be painful if you
want to include very many atoms in the calculation. If the order is
not given in the command, "the atoms within a residue are ordered
first by name, and where these are identical, by alternate location
identifier, and where these are also identical, by serial number" as
You can see command manual pages using the "help" command, e.g.:
What approach is best depends on your particular case -- whether
these are multi-residue macromolecules or single-residue small
molecules, and how many atoms you want to include in the
calculation. If they are single-residue small molecules, you might
just modify the mol2 files so that the atoms you want to pair have
the same names in the two structures (but unique within a structure).
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Jan 15, 2010, at 2:11 AM, Victor Muñoz wrote:
> I want to calculate the RMSD between two mol2 structures in place.
> The two structures are different forms of the same structure. I
> haver modified the mol2 so that the two of them have the same
> serialNumber in their respective atoms. The problem is that when I
> use the command rmsd #model1 #model2, it return an incorrect value
> of the rmsd, as the value showed is too high, about 5, when it
> should be about 1 (the two structures are very similar). Is there
> any way to calculate the RMSD value in place correctly or I am
> doing anything wrong?
> Thanks for your help.
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