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 to provide advice on that.

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@cgl.ucsf.edu http://www.cgl.ucsf.edu

On Mar 7, 2007, at 12:13 PM, Tom Goddard wrote:

I didn't understand your explanation of why 4 points are needed for an alignment with the match command. It looks like only 3 are needed for a unique match. In your example with points ABC and DEF you suggested that the match could either pair A with D, B with E, and C with F or it could pair A with F, B with E, C with D. But the match command specifies the desired pairing so only one of those is possible for any match command invocation.

Tom's right in that with the correspondences specified, 3 points is enough for a unique superposition. After some investigation, it turns out that back in MidasPlus we used a different superposition algorithm and that algorithm required at least four points to work. Chimera uses a different algorithm -- and there is no minimum! It will work with one point. So the 4-point minimum is an unnecessary restriction and will be removed in future releases (though it will warn about non-uniqueness if you use less than 3 points). Navnit, I can send you a file with the restriction removed if you want. Let me know. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu

Hi Navnit, Here is Python code that adds a keyboard shortcut to move selected markers to the local map maxima. https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=prerelease/markpeak.zip This zip file contains a directory MarkPeak that you place in your Chimera distribution in chimera/share It adds a keyboard shortcut "mx" that moves selected markers to the local maximum. You enable keyboard shortcuts with menu entries Tools / General Controls / Accelerators On I have tested with Chimera versions 1.2318 and 1.2352. Tom