Hi Thomas, (1) Currently to transform one structure relative to another, they need to be in separate files, so first put chain A in one PDB file, chain B in another. (2) Then, decide how to match (superimpose) the structures. There are several options - MatchMaker (which will figure out the correspondences for you by doing a sequence alignment and then matching alpha-carbons), the "match" command which will allow you to name the specific atoms you want to use for fitting, both with or without fit iteration (pruning far-apart pairs from the fit). Usually the MatchMaker defaults, which include fit iteration, work quite well - thus I usually try those first. (specific example below) Make note of how the match was done once you are happy with it. (3) Assuming you have rotated and translated things around in order to look at the match, you next want to reset to untransformed positions (at least of the A chain) and re-match with the approach worked out earlier. Then write the matrices to a file or the Reply Log as desired. Specific example: PDB entry 1zik is a leucine zipper with A and B chains. With text editing, I created zika.pdb (just the A chain) and zikb.pdb (just the B chain). In chimera: - open zika.pdb - open zikb.pdb command: mm #0 #1 (this is the command version of MatchMaker, using defaults and zika=#0 reference, zikb=#1 structure to match) I decide this match looks good by rotating/translating and visual examination. Then reset, re-match, write matrices. command: reset (now don't rotate/translate!) command: mm #0 #1 command: matrixget - (the "-" sends the info to the Reply Log. could also write to file) Here is the info pasted from the Reply Log, which is under Favorites in the menu: Model 0.0 1 0 0 0 0 1 0 0 0 0 1 0 Model 1.0 0.318155 -0.0547522 0.946456 7.3815 0.0202055 -0.997713 -0.0645095 35.85 0.947823 0.0396477 -0.316321 -9.44741 The "matrixget/matrixset" man page has more information on the matrices: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 8, 2007, at 5:19 AM, Thomas C. Marlovits wrote:

Hi, am looking for an analysis tool in Chimera that would write out - let's say a matrix for translation/rotation of a pdb-file in respect to another one.

Usage: would like to align chain A and chain B present in a pdb- file and want to know which translation/rotation matrix has to be applied in order to convert the non-aligned pdb-coordinates of chain B to the 'new" aligned pdb-coordinates.

Thanx for your help, -Thomas ---------------------------------------------------------------------- --------- Thomas C. Marlovits, PhD, M.A.S. IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe