Hi Chris, The "write file" capability is actually already implemented in our working version and will be available in the next release (likely in the neighborhood of Oct/Nov). The man page for that command is

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html

Basically, you will be able to write a PDB file of a model in transformed or untransformed coordinates. 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 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=