Dear Jim, If you have a UNIX system, the "pdbrun" command may be able to do what you want. Only the transformed coordinates are written out. I recommend the "nouser" keyword to avoid getting a lot of extra information in USER records. If there are multiple models, they all get sent to one file with END records in between (some postprocessing may be required). example usage: pdbrun all nouser cat >file.pdb See http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pdbrun.html The "write" command is much better for this purpose (and works for all of the platforms) but is not in the current release. It has been implemented in our working version and will be available in the next release. See http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html I am not sure when the next release will come out, however. Finally, I believe there is a way to get the transformation matrices but I must defer to the programmers on the team to address this point. I hope this helps, Elaine =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elaine C. Meng, R.Ph., Ph.D. Babbitt Lab and Computer Graphics Lab meng@cgl.ucsf.edu http://www.cgl.ucsf.edu/home/meng/index.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=