On Sep 15, 2008, at 3:13 AM, julien(GWDG) wrote:

I wanted to know if there is a way in chimera to get the same information as the shortcut ai but for small molecule. When I use "ai" with small molecule I get the message : "not enough back bone atoms", which is normal because there is no back bone atom and because the molecule is small. But I have a rigid docking of one ligand and I would like to see what is the rotation components (rotation matrix) between the different pose. Of course one could just do it by a small C++ script but if chimera has it already implemented it would be easier for us.

Thank you for your support and your nice soft.

many greetings

Julien

Hi Julien, Thanks for the compliments! There are commands to do a similar thing, although not in one step. The "match" command will fit the specified atoms and give an RMSD. Unlike the ai shortcut, it moves one structure onto the other. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> Then you can use the "matrixget" command to report the transformations of the structures. However, note this reports the total transformation: all movements that have been applied, not just what happened in the fitting step. To get only the fitting transformation, you would first need to "reset" the reference structure so it is untransformed, then "match" the other structure onto it, then use "matrixget." <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html> For example, using two different structures with FAD: open 1f3p open 2npx focus preset apply int 1 reset match #1:fad #0:fad matrixget - Don't move anything around by hand between "reset" and "matrixget"! The last command sends the matrix info to the Reply Log. In this case the atoms in FAD are ordered and named consistently, so I could simply use the residue name in the match command. If you only wanted to use certain atoms, or if the atoms were not ordered and named consistently, you would have to give the atom names in the match command. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html