On Jul 25, 2010, at 7:15 PM, Thomas Ouldridge wrote:
Hi, I'm afraid I'm not a crystallographer/protein simulator, and so this question might seem quite naive. I run coarse-grained simulations, and I would like to represent the objects as ellipses in chimera. I have the position (which I am able to use) and the orientation that I would like my ellipses to take, encoded as a matrix relative to (x,y,z) cartesian coordinates. This matrix gives me the principal axes and radii of the ellipse.
As I understand, Chimera is designed to display a "Thermal ellipsoid" - I would like this ellipsoid to have the axes and radii given by my matrix. However, it seems that the input (via pdb format files) is interpreted as an "anisotropic temperature factor", and I can't find a way to convert my matrix into the anisotropic temperature factor (I tried some papers online but they seemed to be talking in terms of transformations between lab frame and crystallographic frames, but I cannot see how that applies - what is my crystallographic frame?).
In short, is there a way to convert my matrix into the "anisotropic temperature factor" representation so that Chimera can read it and convert it back? I did try just plugging in the matrix elements to the PDB file but got some weird ellipsoids out.
Hi Tom, The ANISOU record uses the same coordinate frame as the ATOM records, so you should be able to just plug in your matrix values. There are a couple of tricks though. First, the ordering of the six numbers in the ANISOU record is (1,1), (2,2), (3,3), (1,2), (1,3), (2,3), i.e. first the main diagonal: (1,1), (2,2), (3,3) then filling out the first row: (1,2), (1,3) then finally the third element of the second row: (2,3). Also, the values are integers, and are divided by a factor of 10000 to get the final values. Is this what you tried? It should also be possible to directly assign to the atom's anisoU attribute using a Python script if the above doesn't work for some reason. Let me know if you need that. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu