# [Chimera-users] RMSD fit of an object to atom

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 7 11:55:22 PST 2007

```On Mar 7, 2007, at 10:45 AM, Navnit Kumar Mishra wrote:

>
> Dear folks;
>
> Is there any simple way in chimera to do rmsd fitting of the object to
> the atom. I would like to measure the rmsd of an density peak with the
> atom. Could someone give the detail, how can I do it.

Since the RMSD between a single peak and an atom is the same as the
distance, you can use the Volume Path Tracer tool to drop a "marker"
on the density peak and then measure the distance from the marker to
the atom (control click the marker [selecting it] and shift-control
double-click the atom [selecting it also and bringing up a context
menu] and choose "Show Distance").  I don't know if once you've
dropped the marker near the peak if there is any way to migrate it
automatically to the absolute peak.  Perhaps Tom Goddard will be able

> And one another
> thing, how can I get rid of the problem with " At least four atoms
> should be selected", I am interested to do 'match' for two atoms.

There is no unique transformation between coordinate systems unless
you specify a non-planar set of points (i.e. at least 4).  With only
two, you are basically specifying two axes that you want to be
collinear.  Not only are there two ways to make them collinear, but
there are an infinite number of relative rotations possible about the
collinear axes.

With three points, the non-uniqueness problem is a little less
obvious.  Consider two sets of points A-B-C and D-E-F that form right
angles.  Clearly you can superimpose A-B-C with D-E-F in a 1-to-1
fashion.  But you can equally validly superimpose A-B-C with F-E-D
(i.e. 180 degree flip).  So... you need 4 points.

If you don't care about the non-uniqueness, you can use the "align"
command to place both pairs of atoms on the Z axis, with one atom of
each pair superimposed.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab
pett at cgl.ucsf.edu
http://www.cgl.ucsf.edu

```